[English] 日本語
Yorodumi
- PDB-4x65: Crystal Structure of 30S ribosomal subunit from Thermus thermophilus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4x65
TitleCrystal Structure of 30S ribosomal subunit from Thermus thermophilus
Components
  • (30S ribosomal protein ...) x 20
  • 16S rRNA
  • RNA (5'-D(*AP*(MA6)P*AP*UP*UP*U)-3')
  • RNA (5'-D(P*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*(PSU)P*C)-3')
KeywordsRibosome/antibiotic / 30S ribosomal subunit m6A decoding mRNA modification / Ribosome-antibiotic complex
Function / homology
Function and homology information


small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding ...small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A ...Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S3, C-terminal domain / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal Protein S8; Chain: A, domain 1 - #30 / RNA-binding S4 domain / Ribosomal Protein S7 / Ribosomal protein S7/S5 / Ribosomal protein S6/Translation elongation factor EF1B / Ribosomal protein S3 C-terminal domain / Helix hairpin bin / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S15/NS1, RNA-binding / K homology (KH) domain / Double Stranded RNA Binding Domain - #20 / Helicase, Ruva Protein; domain 3 - #50 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Ribosomal Protein S5; domain 2 - #10 / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / GMP Synthetase; Chain A, domain 3 / Ribosomal Protein S5; domain 2 / Double Stranded RNA Binding Domain / Ribosomal protein S14, type Z / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Few Secondary Structures / Irregular / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / KH domain / Ribosomal protein S2 / Type-2 KH domain profile. / K Homology domain, type 2 / : / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S5, N-terminal, conserved site
Similarity search - Domain/homology
: / PAROMOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 ...: / PAROMOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / 30S ribosomal protein S17 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
Thermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.345 Å
AuthorsDemirci, H. / Chen, J. / Choi, J. / Soltis, M. / Puglisi, J.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM51266 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM099687 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: N(6)-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics.
Authors: Choi, J. / Ieong, K.W. / Demirci, H. / Chen, J. / Petrov, A. / Prabhakar, A. / O'Leary, S.E. / Dominissini, D. / Rechavi, G. / Soltis, S.M. / Ehrenberg, M. / Puglisi, J.D.
History
DepositionDec 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Feb 10, 2016Group: Database references
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Dec 25, 2019Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 16S rRNA
B: 30S ribosomal protein S2
C: 30S ribosomal protein S3
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6
G: 30S ribosomal protein S7
H: 30S ribosomal protein S8
I: 30S ribosomal protein S9
J: 30S ribosomal protein S10
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
M: 30S ribosomal protein S13
N: 30S ribosomal protein S14 type Z
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
U: 30S ribosomal protein Thx
a: RNA (5'-D(*AP*(MA6)P*AP*UP*UP*U)-3')
b: RNA (5'-D(P*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*(PSU)P*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)786,288394
Polymers772,96023
Non-polymers13,328371
Water4,125229
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area118590 Å2
ΔGint-938 kcal/mol
Surface area278300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)401.440, 401.440, 175.924
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

-
RNA chain , 3 types, 3 molecules Aab

#1: RNA chain 16S rRNA /


Mass: 494170.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#22: RNA chain RNA (5'-D(*AP*(MA6)P*AP*UP*UP*U)-3')


Mass: 1875.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#23: RNA chain RNA (5'-D(P*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*(PSU)P*C)-3')


Mass: 3708.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8

-
30S ribosomal protein ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTU

#2: Protein 30S ribosomal protein S2 /


Mass: 27217.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80371
#3: Protein 30S ribosomal protein S3 /


Mass: 22975.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80372
#4: Protein 30S ribosomal protein S4 /


Mass: 24242.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80373
#5: Protein 30S ribosomal protein S5 /


Mass: 16460.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ5
#6: Protein 30S ribosomal protein S6 / / TS9


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP8
#7: Protein 30S ribosomal protein S7 /


Mass: 17919.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P17291
#8: Protein 30S ribosomal protein S8 /


Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS
#9: Protein 30S ribosomal protein S9 /


Mass: 14279.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80374
#10: Protein 30S ribosomal protein S10 /


Mass: 11398.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN7
#11: Protein 30S ribosomal protein S11 /


Mass: 12606.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80376
#12: Protein 30S ribosomal protein S12 /


Mass: 13921.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN3
#13: Protein 30S ribosomal protein S13 /


Mass: 13365.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80377
#14: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 7027.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ1, UniProt: P0DOY6*PLUS
#15: Protein 30S ribosomal protein S15 /


Mass: 10447.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJ76
#16: Protein 30S ribosomal protein S16 /


Mass: 9995.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJH3
#17: Protein 30S ribosomal protein S17 /


Mass: 11722.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP7, UniProt: P0DOY7*PLUS
#18: Protein 30S ribosomal protein S18 /


Mass: 8497.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLQ0
#19: Protein 30S ribosomal protein S19 /


Mass: 9260.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP2
#20: Protein 30S ribosomal protein S20 /


Mass: 10921.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80380
#21: Protein/peptide 30S ribosomal protein Thx / Ribosome / S31


Mass: 3089.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIH3

-
Non-polymers , 5 types, 600 molecules

#24: Chemical
ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E / Paromomycin


Mass: 615.628 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: Antimicrobial, medication*YM
#25: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 317 / Source method: obtained synthetically / Formula: Mg
#26: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 46 / Source method: obtained synthetically / Formula: K
#27: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#28: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.58 Å3/Da / Density % sol: 73.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2014
RadiationMonochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionRedundancy: 11.9 % / Number: 2438566 / Rmerge(I) obs: 0.135 / Χ2: 0.96 / D res high: 3.35 Å / D res low: 35 Å / Num. obs: 204935 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
9.043510.040.89512.2
7.29.0410.0540.94212.4
6.297.210.0680.9112.4
5.726.2910.080.92113.1
5.315.7210.0870.9313.4
55.3110.0950.92813
4.75510.1090.92311.5
4.544.7510.1260.9112.8
4.374.5410.1490.91613
4.224.3710.1780.91313.1
4.094.2210.2160.92813.2
3.974.0910.2570.91413.2
3.873.9710.3471.2513.2
3.773.8710.3750.96512
3.693.7710.5010.98411.4
3.613.6910.5821.2511.6
3.543.6110.6210.8888.9
3.473.5410.7820.8869
3.413.4710.8771.1049.1
3.353.4110.8899.2
ReflectionResolution: 3.3448→35 Å / Num. obs: 204935 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 65.11 Å2 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.043 / Rrim(I) all: 0.141 / Χ2: 0.962 / Net I/av σ(I): 19.081 / Net I/σ(I): 6.5 / Num. measured all: 2438566
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3.3448-3.419.2101530.7970.3620.889100
3.41-3.479.1101360.8080.3061.1041000.8770.929
3.47-3.549101550.8730.2730.8861000.7820.829
3.54-3.618.9101340.9020.2180.8881000.6210.659
3.61-3.6911.6101760.9240.1771.251000.5820.609
3.69-3.7711.4101230.9520.1550.9841000.5010.525
3.77-3.8712101610.9670.1120.9651000.3750.392
3.87-3.9713.2101630.9740.0991.251000.3470.361
3.97-4.0913.2101970.9850.0730.9141000.2570.267
4.09-4.2213.2101960.9880.0610.9281000.2160.225
4.22-4.3713.1101870.990.0510.9131000.1780.185
4.37-4.5413102090.9930.0430.9161000.1490.155
4.54-4.7512.8102170.9940.0360.911000.1260.131
4.75-511.5102380.9940.0330.9231000.1090.114
5-5.3113102760.9960.0270.9281000.0950.099
5.31-5.7213.4102810.9970.0240.931000.0870.09
5.72-6.2913.1103150.9970.0230.9211000.080.083
6.29-7.212.4103720.9970.020.911000.0680.07
7.2-9.0412.4104510.9980.0160.9421000.0540.056
9.04-3512.2107950.9980.0120.89599.70.040.042

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1938)refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementResolution: 3.345→34.959 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2104 10261 5.03 %
Rwork0.1841 --
obs0.1854 204105 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.345→34.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19119 32875 617 229 52840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00556721
X-RAY DIFFRACTIONf_angle_d0.77984150
X-RAY DIFFRACTIONf_dihedral_angle_d19.17526747
X-RAY DIFFRACTIONf_chiral_restr0.04210584
X-RAY DIFFRACTIONf_plane_restr0.0245155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3448-3.38270.30253140.26045914X-RAY DIFFRACTION92
3.3827-3.42250.30673340.26486248X-RAY DIFFRACTION97
3.4225-3.46420.26423400.25826322X-RAY DIFFRACTION98
3.4642-3.5080.25293210.24596394X-RAY DIFFRACTION99
3.508-3.55410.25973360.23916384X-RAY DIFFRACTION99
3.5541-3.60280.24883560.22576399X-RAY DIFFRACTION100
3.6028-3.65420.26373540.23456420X-RAY DIFFRACTION100
3.6542-3.70870.25773400.24666411X-RAY DIFFRACTION100
3.7087-3.76660.25143350.20976446X-RAY DIFFRACTION100
3.7666-3.82820.23153310.20146468X-RAY DIFFRACTION100
3.8282-3.89420.24673480.20376430X-RAY DIFFRACTION100
3.8942-3.96490.23923180.20056437X-RAY DIFFRACTION100
3.9649-4.0410.21983370.18336455X-RAY DIFFRACTION100
4.041-4.12340.20923220.17646480X-RAY DIFFRACTION100
4.1234-4.21290.19653410.17936489X-RAY DIFFRACTION100
4.2129-4.31070.18583340.176441X-RAY DIFFRACTION100
4.3107-4.41830.20243260.17186500X-RAY DIFFRACTION100
4.4183-4.53760.19953420.16996452X-RAY DIFFRACTION100
4.5376-4.67080.19153560.16366490X-RAY DIFFRACTION100
4.6708-4.82120.18813440.15946461X-RAY DIFFRACTION100
4.8212-4.9930.18813680.15766466X-RAY DIFFRACTION100
4.993-5.19230.1923520.15046500X-RAY DIFFRACTION100
5.1923-5.42780.16423470.14796499X-RAY DIFFRACTION100
5.4278-5.71280.17863490.14416524X-RAY DIFFRACTION100
5.7128-6.0690.17733580.14916546X-RAY DIFFRACTION100
6.069-6.53480.18243630.15746530X-RAY DIFFRACTION100
6.5348-7.18730.18083450.14736573X-RAY DIFFRACTION100
7.1873-8.21550.16363480.14986603X-RAY DIFFRACTION100
8.2155-10.30650.19813630.17496668X-RAY DIFFRACTION100
10.3065-34.96090.223390.20336894X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.54250.222-0.26020.3734-0.12580.34020.04-0.01180.03790.13710.06230.09260.09230.0129-0.10440.52190.07950.02910.449-0.01930.594144.113883.7141-12.4889
21.5488-0.14590.12550.53120.08410.26480.0449-0.71020.49460.3136-0.0156-0.0386-0.12580.1246-0.03280.7328-0.23880.1481.1868-0.48960.7915222.6305129.85289.1823
31.18070.471-0.5240.0335-0.27040.1387-0.1538-0.0786-0.3552-0.10540.1374-0.18260.1958-0.02160.01190.63070.0167-0.01250.6015-0.03180.7679163.536869.5575-25.7419
44.8481-3.0793-2.84821.99611.75721.83290.83331.14841.3956-1.0171-0.4747-0.9028-0.36360.5758-0.27121.23050.13660.26272.65140.20181.583203.862112.2801-33.5301
56.3023.57533.06625.116-2.95258.63560.17480.20270.7028-1.4023-0.0298-1.2266-0.80710.3495-0.10881.15260.11380.34890.6991-0.06811.2345156.987156.256-36.4226
62.2434-0.81570.63674.77964.08089.32560.22050.02720.5939-0.6529-0.34630.7611-1.4639-0.92950.14561.08290.09240.28960.62130.0141.5872149.8886156.5421-28.1127
74.57061.40481.40936.7998-3.35036.8440.14060.12051.4854-0.8069-0.059-1.1142-2.01971.2341-0.09681.2282-0.18150.39120.7488-0.08371.4224166.8803163.1326-19.6736
80.96290.97450.623.29510.33113.990.0179-0.16730.38760.2420.2344-0.2162-0.5760.3577-0.19110.9271-0.24180.51730.793-0.51641.5099174.0925158.0582-7.4371
99.46282.82963.44074.6375-0.00711.5705-0.58810.27970.94780.5710.3134-0.7178-1.02741.46870.29431.4412-0.47470.2221.4258-0.55961.766190.274162.8714-5.3596
100.8823-0.42390.49031.8938-0.46951.1730.0394-0.0250.6577-0.61040.0984-0.0062-0.6384-0.02860.07131.18250.00010.44550.5132-0.19091.5439160.1144156.9973-19.0736
112.60742.01840.82589.5721-1.99171.12571.1829-0.05711.6581-0.4761-0.1425-0.1275-2.3746-0.1892-1.08372.222-0.03240.43380.79430.00882.5092163.2222175.0424-23.946
120.1624-0.1617-0.0070.3807-0.11290.066-0.0623-0.5710.26020.68690.02790.009-0.1596-0.1764-0.09331.1638-0.11940.20071.7682-0.75941.0465205.4214142.646233.158
130.4482-0.3993-0.34971.07430.41980.8271-0.1562-0.2890.1430.21510.00090.32850.0156-0.2894-0.03610.7159-0.21270.32591.5184-0.71250.9819190.0317134.012317.414
145.7518-5.0266-3.43125.26560.86637.79470.0804-0.64080.44110.82170.54630.43980.12640.2874-0.59290.9495-0.12260.03730.8162-0.09830.6134155.7517111.305337.715
154.1845-0.85843.55721.73351.35965.88130.281-0.33760.68760.2909-0.1217-0.4054-0.80740.9238-0.11670.9261-0.20630.02480.679-0.12920.651161.703113.09425.3724
162.22480.08610.54582.5665-2.55373.8910.1578-0.10040.15120.2236-0.12960.1720.1509-0.0996-0.03280.85860.03180.14910.5342-0.1290.5992137.5135103.900231.2687
173.5604-2.95331.9786.41710.56852.3352-0.1731-1.40290.36161.55170.37190.7259-0.6818-0.3847-0.10571.292-0.02370.36560.9945-0.23550.8228133.9312110.0547.8729
187.95154.6313-5.24225.7577-4.02634.86980.62490.24791.0919-0.19680.140.2976-1.0372-0.2763-0.69140.81310.10360.02260.5142-0.140.6488140.8302114.222423.7314
194.0046-5.1103-2.96779.51340.24166.5605-0.8321-2.13320.52961.50790.61280.7632-0.00230.09680.14450.5312-0.05460.14031.2318-0.32570.9717162.1694127.25287.923
204.57681.542-0.15961.0843-0.45791.45770.3211-0.19410.26740.18580.1967-0.3759-0.36130.7665-0.47330.5533-0.14460.09410.9452-0.37290.8028184.1198122.8022-2.7599
213.1995-2.2936-3.19983.2811.11634.2131-0.0781-0.57280.44690.21020.28070.10440.0710.1245-0.11340.5684-0.06630.28790.5903-0.31430.8583162.0609129.95144.3388
225.0751-6.53453.62469.3998-3.85063.859-0.253-0.19781.06320.27310.2118-0.4291-0.52560.56160.06030.6276-0.18110.21430.7279-0.30130.9078167.8919133.91875.148
238.90632.52080.53875.89641.27162.1364-0.0211-0.22370.43040.0270.01590.0414-0.3422-0.1694-0.00920.56260.08480.21810.6204-0.18921.0756145.3615129.66160.325
243.3266-0.3884-4.57870.25140.36496.5652-0.47041.4234-1.6062-0.1028-0.27170.54320.729-0.80950.67730.41380.07080.1820.6388-0.17450.9439152.6626120.4149-10.9774
251.8344-1.23990.00471.51820.52230.6292-0.1458-0.1728-0.27260.3191-0.01760.50610.2292-0.25480.18040.59420.07150.29680.4333-0.13330.8769145.8165117.09670.8423
262.8333-1.91220.68093.98811.45291.53490.0672-0.07450.20190.3312-0.07560.18380.1648-0.0283-0.02740.4537-0.0060.17130.4697-0.1630.6478153.4211121.1607-0.5953
276.94262.9122-1.13063.39142.28145.978-0.00420.00790.8236-0.1994-0.36810.6977-1.2497-1.28680.25850.77090.23370.26210.7094-0.15651.0741136.6079134.2696-9.5213
285.75680.8535-3.48973.43450.68872.744-0.30721.7261-0.1452-1.03820.04830.1804-0.105-0.62120.2011.03160.1202-0.07191.6870.12330.567173.9127114.6357-93.9468
297.13940.44953.82114.92110.90166.05490.23251.29990.0971-0.6788-0.0372-0.0115-0.2845-0.4093-0.17910.7630.16460.11641.27020.13150.5839174.8481115.673-87.598
305.95925.83665.69215.75615.65065.5993-0.6822-0.6061.7755-1.4362-0.67992.2134-1.4696-1.10391.38380.91220.2795-0.04051.22840.34011.3772165.7651131.7186-73.9675
317.77735.458-1.15433.9403-0.90060.32440.3028-0.85432.60750.3651-0.6431.6572-0.4043-0.40970.29460.7875-0.11810.06480.9178-0.35891.4448217.7301143.0852-23.948
329.73735.6955-6.52993.332-3.81474.4208-0.39430.404-1.1232-0.0379-0.08790.09620.6498-0.55830.47360.848-0.09230.08840.7818-0.1751.5659239.701152.4236-25.7367
333.5488-0.61892.02696.2611-3.15786.2925-0.21640.02870.674-0.16030.0369-0.5325-0.5120.86790.23430.6339-0.27440.19440.8183-0.25341.0633245.3048143.05-23.5679
340.13270.6515-0.57749.6525-3.49025.0729-0.2765-0.0250.12520.0065-0.15550.3709-0.1126-0.15850.40870.9827-0.44010.37941.5325-0.16761.8124253.7199146.8602-38.0485
352.79420.03314.0988.65663.48177.3986-0.14230.96030.8718-0.3343-0.13680.42390.2458-0.05430.21440.71250.08470.17011.0469-0.02810.7046233.3332136.471-38.203
367.79174.83781.17977.8404-0.6982.11710.7011-1.17810.06921.7322-0.73921.0380.8902-0.57570.04721.2529-0.00590.02771.1379-0.16160.8095219.5674124.6927-39.3412
377.6112-1.41121.31880.9370.60431.3226-0.1508-0.16730.0442-0.21150.2189-0.11760.0164-0.2417-0.07310.5832-0.16140.14920.7797-0.10771.0083235.1596135.6561-31.4719
386.5779-4.72696.43925.5214-3.96676.51640.20171.02780.3645-0.34610.0115-0.36730.12571.401-0.11760.6627-0.12020.27930.9471-0.14490.9686250.7693134.1872-31.1184
395.09435.30323.73767.03971.25968.2703-0.41632.2842-2.4397-1.25830.7814-1.2780.7150.4996-0.28420.83860.01830.07060.8924-0.22180.9186237.7883128.2785-40.9267
406.965-1.1705-0.08086.82811.89512.1080.4857-1.88972.78151.4378-0.21870.7378-2.521-0.9516-0.32761.19860.10050.08951.3107-0.43681.4062219.6007125.2376-44.9832
412.65372.00461.81938.036-1.06972.16960.28310.1404-0.7035-0.38650.295-0.06420.04730.1408-0.41670.35570.08090.16640.47810.01410.7935140.0807123.1463-30.8851
428.13533.51316.91323.04923.30545.9623-0.091-0.15210.9039-0.3866-0.34230.5027-0.7469-0.61240.44450.49040.11970.25690.54930.04970.983139.1144132.8096-32.0858
432.5212-3.176-3.36298.95867.54617.80350.06710.19910.0065-0.0115-0.38221.3788-0.3476-0.80950.28670.61420.10010.24680.47610.18611.1006126.5146126.2218-27.7663
441.6915-1.87341.57824.00450.29793.97380.010.09130.4585-0.25530.11390.2226-0.4226-0.317-0.10960.5320.08910.14620.55490.13341.3344130.3578133.5574-30.2101
458.8311-2.8462.66645.69712.68043.58310.48171.01130.1424-0.7142-0.3972-0.3191-0.31160.1323-0.08880.47990.21650.05270.5970.24570.9864133.3113132.2532-39.0528
462.6407-0.55881.56584.59851.98073.85350.0036-0.48620.73090.12040.3696-0.4426-0.49070.0386-0.28950.57760.03520.27420.4825-0.0911.3744145.3657140.7723-17.3596
476.50754.0232.14773.112.05553.34060.0413-0.53020.1410.09130.3364-0.4013-0.032-0.0167-0.36450.53940.08510.2370.45980.02231.0104143.3131130.0181-19.0512
480.7953-0.07010.54721.3506-1.01431.0706-0.0060.1118-0.04970.08880.1173-0.0620.18960.0958-0.08420.40840.10010.13170.3453-0.01490.8144134.0156109.2626-24.5516
491.7342-1.56352.22212.1067-1.283.5978-0.36150.4369-2.226-0.303-0.0188-0.6521.55971.25560.38230.5280.03440.06840.6416-0.11911.0571125.5412110.1576-12.4317
505.1684.44665.92324.19765.57498.03940.8297-0.5332-2.33130.9993-0.7026-1.4712.0269-0.2105-0.09430.7944-0.0670.00320.54760.02011.2383134.1985119.8863-8.9827
512.73460.32951.43582.91682.5973.0002-0.0435-0.44820.19560.08960.08230.1513-0.0184-0.1578-0.01090.45460.16420.23310.55780.15360.7558126.2423119.3101-19.1405
528.1914-5.2654-0.49245.3707-2.39518.1871-0.3845-1.03181.56840.28360.4214-0.8393-0.59490.0836-0.10730.42310.05380.19380.5089-0.11581.1376122.4363120.362-15.6976
530.25880.45720.30915.642.52773.57850.3086-0.0821-0.2449-0.12640.3386-0.3717-0.07390.3799-0.6140.44340.1490.17610.58850.08530.7833131.2256117.7038-19.2094
541.8305-1.48360.81553.38621.87343.28880.1414-0.15610.5792-0.232-0.2364-0.3648-0.86720.1540.18671.0768-0.35330.30081.0107-0.51741.7318239.6732167.0327-5.3605
551.8034-0.48161.80944.794-5.83077.94620.02670.3672-0.29030.5096-0.4553-1.5378-0.88371.43230.4540.9198-0.4976-0.0161.0755-0.34021.7283250.2058162.0953-4.6833
561.33232.6511-1.99596.7203-2.81094.3855-0.38810.55680.2256-0.4551-0.1289-0.3591-0.15960.84580.51710.8907-0.33820.30221.0053-0.35571.4804245.0556158.776-14.1634
572.3133-0.42042.15913.67740.03732.8456-0.27260.30940.64030.1570.0791-0.3424-1.01440.63590.2970.9791-0.37110.18710.8246-0.35941.6209239.8649165.0693-9.1631
580.45221.65130.66769.32822.60260.9949-0.15740.59970.8871-0.74210.2005-0.0023-0.82290.3511-0.0371.1143-0.20450.11260.9572-0.10391.8179229.8251172.7973-17.9342
592.03070.38570.39060.76240.02531.11730.0552-0.27370.9038-0.01920.03540.1163-0.42110.1097-0.15240.7239-0.36380.29841.1087-0.51591.1299226.0648147.849-6.8766
605.9151-2.88662.64571.4203-1.59368.1910.31710.4093-0.8257-0.0232-0.17070.27811.3073-0.4976-0.18770.7915-0.1732-0.02591.2891-0.61250.7112222.5203124.6037-7.242
614.02783.12321.83672.79640.87381.6350.2973-0.41821.02841.044-0.44390.1191-0.74040.01940.25041.1899-0.26550.10051.6748-0.88261.6673222.3055163.561926.1304
620.65-0.78021.03260.9374-1.11476.6295-0.0172-0.69751.07791.2956-0.19780.355-1.61-0.31590.33921.4431-0.42670.14281.5185-0.941.7376227.9127166.901422.2403
633.31711.6665-1.39312.2782-2.46062.7389-0.0499-0.00750.10170.19070.00960.1384-0.02350.11490.02310.9609-0.04810.27111.4721-0.47841.1418225.3207143.078416.7485
640.3252-0.1130.33860.27520.22020.8353-0.0676-0.24410.2972-0.46250.2476-0.3666-0.5818-0.0279-0.12390.8716-0.26210.22541.2997-0.570.8778218.2462136.314912.8735
652.520.37044.8317.15192.09819.5347-0.6465-1.08311.03390.9482-1.03791.0796-2.0415-0.9381.70041.6896-0.56550.18291.8124-1.15192.0813231.2754170.4429.6298
660.8694-1.1484-1.95983.80033.36594.6804-0.4211-1.11960.63790.791-0.89981.3877-0.1676-2.12461.33561.9867-0.16570.16791.9539-0.9781.3883224.4532173.080138.5274
675.14422.07265.17722.01852.04135.2120.6163-2.99032.58631.6127-1.44571.5246-1.6651-2.34810.83661.51530.00850.28052.1301-0.51391.7565216.4863161.391134.4576
685.47613.48482.73423.13290.99491.9708-0.31160.5766-0.86640.67411.4758-1.9337-0.41422.2373-1.21771.62440.05190.01341.8291-0.95531.4646228.3157157.742232.305
693.6157-1.30462.3528.431-2.31192.75270.15990.78090.3609-0.61390.3787-0.2169-0.23090.2418-0.45550.4795-0.03910.18680.9324-0.0880.7933213.2195118.7239-69.698
702.9733-0.2784-1.13812.28330.30322.0723-0.02010.21990.07490.06340.0709-0.35450.05270.9402-0.07280.52290.05430.21590.8446-0.03410.7208217.4555114.9662-63.0585
716.67831.545-4.35434.9552-2.81878.8585-0.25860.47030.3767-0.52420.077-0.77190.14690.96970.140.45690.00180.19490.7493-0.02950.8983221.4754122.0621-65.003
722.02172.29422.80778.4456-0.04548.8350.1062-0.66170.9080.2661-0.45670.3516-0.58790.36590.34630.5957-0.03220.17960.8288-0.12910.8189211.5714125.9792-65.255
732.84460.30324.0714.46824.36199.5011-0.22521.04041.1308-0.8813-0.254-0.8582-0.81830.83680.51570.7833-0.00570.19220.73510.27440.8885211.1509129.7349-70.2561
741.8472-2.21472.48845.8445-3.0333.45850.02690.15230.217-0.00960.1779-0.2964-0.3357-0.1397-0.22170.47760.07240.22630.7252-0.13770.8411193.8153110.6059-58.12
755.6218-4.01846.71843.1314-4.82317.99190.2473-0.2443-0.4875-0.16660.30120.43140.4243-0.1226-0.52010.28070.11840.02940.46720.00290.5559153.44789.4442-13.8149
765.93020.7312-0.575.8905-0.45233.0529-0.0439-0.2161-0.4470.30620.1263-0.42970.57370.7578-0.05550.55080.1568-0.09170.70320.00230.607174.976279.36599.7178
773.71170.53174.40199.6374-2.4267.8730.1983-0.5917-1.8898-0.65920.91162.83471.0686-0.9352-1.17890.6645-0.12410.08041.3675-0.1261.5433273.712115.4281-8.6386
783.067-2.67483.10984.3404-5.60567.6316-0.0207-0.29720.86820.11840.20511.534-0.3398-0.7363-0.17590.3770.0299-0.03140.9976-0.09260.8734268.4674119.9388-5.6522
796.86085.023-3.54445.2425-3.25553.48770.1315-0.6477-0.03140.3294-0.3492-0.6636-0.33990.69860.21550.5664-0.2035-0.03721.2508-0.25891.1286275.6397121.6856-1.5153
805.73685.43-3.14445.1585-2.97111.72440.5706-1.2159-1.15011.0442-0.7998-1.433-0.43991.00140.22740.7653-0.1149-0.13471.5006-0.13390.9444264.8333104.51999.0676
817.0262-6.95311.62247.0728-2.36785.74950.168-0.1679-0.13460.6615-0.2389-1.3211-0.26620.98730.09350.6732-0.262-0.08381.4833-0.07950.9587249.119999.180913.9119
824.31523.52164.92017.08243.33878.80170.2372-0.5853-0.41230.43940.3435-0.08650.09920.7889-0.61370.5578-0.02460.02721.2474-0.11830.6272240.1217103.6892.4543
833.7564-0.7462-2.20334.64274.59435.1417-0.0581-0.35480.08790.94390.1514-0.3047-0.35690.1974-0.11231.1141-0.01350.02351.5762-0.41250.8294220.0061118.318433.7797
849.7349-8.1062-7.4427.3446.45755.8034-1.8813-4.061.38813.50732.04280.63130.7570.703-0.22481.1963-0.13840.05871.8983-0.16731.0094231.9116120.35739.355
850.01760.0384-0.19252.546-1.63738.22650.0937-0.08780.2010.28550.0662-0.1511-0.42080.6628-0.19190.8346-0.38950.18621.4912-0.26970.6303228.0289122.317530.2912
860.3682-1.2711-1.66346.89756.14457.5838-0.1904-0.06420.04720.38090.5407-0.45770.99181.2881-0.39230.7594-0.26940.10871.3994-0.33950.4768215.3871126.074526.4611
870.2708-0.2512-0.73591.96211.11973.35960.0731-0.14580.39780.1694-0.11350.08210.19110.1426-0.06060.7064-0.17280.14421.2479-0.57760.8756216.6267135.46719.6441
885.50145.7549-5.61546.0328-5.98887.8615-0.30693.30041.0946-1.69380.49450.3933-0.367-0.5833-0.21340.99190.23020.02481.33310.17190.9662141.4433110.8774-74.4085
892.47-3.55670.87856.70841.04153.86390.49550.6864-0.5115-0.75710.0080.3741-0.2512-0.1341-0.44080.52020.0677-0.07480.88630.14350.6934144.9823104.494-66.857
904.7539-2.7331-0.0543.66870.61912.62660.1155-1.3722-0.5760.17720.14240.21750.06560.0136-0.2350.4299-0.0189-0.06110.88030.11410.681143.7186102.1127-56.6759
914.1122.7519-3.31438.86733.04197.40660.4746-0.0603-2.59030.1172-0.479-0.0481.35010.0836-0.10740.62710.0829-0.35321.08890.1541.1519131.266597.9467-64.3031
923.1981-1.60281.27851.0717-0.40093.4593-0.0864-0.41470.14150.43930.21840.0110.0632-0.1069-0.11480.7001-0.00410.27930.45870.00660.6876118.452377.060215.6197
931.2114-0.72890.10362.66650.70182.08670.0493-0.15150.4937-0.14630.133-0.0191-0.42120.2694-0.14310.589-0.0450.18670.41390.01610.8019115.912377.476811.1645
943.47741.6453.29680.80531.56163.7115-0.1509-0.38521.2497-0.50830.038-0.0322-1.6701-0.41070.11290.97930.15510.40340.5461-0.05731.0624110.825686.630721.3105
951.98841.23520.27460.93710.77472.2193-0.1829-0.03330.41770.0169-0.08590.7966-0.9977-0.33160.27160.65630.11810.14630.45820.17341.1161101.781379.70366.4196
968.34085.87145.60657.34211.03056.4289-0.0604-0.744-0.23350.6391-0.07680.6732-0.0629-0.39140.07130.7175-0.0290.35360.45740.12570.8697102.159975.301817.234
972.46951.5391-0.5886.31980.04961.2841-0.11160.60020.292-0.65230.23750.0987-0.3259-0.0644-0.12460.6448-0.0416-0.15210.58610.16270.722120.110381.308-38.112
982.96782.16090.7884.00881.37021.8365-0.32160.25560.0644-0.62960.34580.4194-0.091-0.1855-0.02370.5336-0.0857-0.00710.5580.14390.6095122.093485.1225-35.3476
993.8219-5.14784.12628.1605-4.64815.14040.46181.60310.7224-0.8006-0.4677-0.97280.22260.66930.0340.85-0.16110.12171.138-0.00780.8633138.033785.951-44.4595
1005.6416-5.66090.31026.1256-2.12128.4391-0.14440.26882.68070.5288-0.3605-1.7998-1.95080.90750.55891.24580.06610.29550.64430.22891.3186180.9772140.1934-64.4692
1014.4926-3.3507-3.69496.65842.01893.17470.02740.0466-0.118-0.56480.10930.2628-0.1586-0.1299-0.13281.70840.09910.24410.80870.22351.6361175.3613141.229-72.0496
1023.4486-3.0287-4.42752.66013.88585.75830.06120.39280.2016-0.8718-0.0058-0.7205-0.42920.395-0.11140.82920.11360.18451.34290.32481.0061172.6623129.252-77.2858
1033.39662.25541.49655.17516.19638.06810.10892.03831.9834-2.36730.0714-0.9357-2.91351.2045-0.21621.02550.1240.32571.03320.37091.0744181.4099133.0707-74.9573
1045.9304-5.4599-5.90435.05635.57256.56450.4977-0.1150.2291-0.62770.0099-2.3053-0.01062.3263-0.50160.64610.10510.08670.9219-0.01430.8731186.6543128.5511-66.532
1055.8938-1.4855-3.52996.74353.71465.42960.27210.12360.48240.33190.0586-0.0366-0.353-0.2822-0.24220.70610.08730.2240.71270.20890.5791175.9792127.2556-67.5504
1065.34513.66020.00236.44391.54681.12670.02450.48860.02310.24620.6842-0.5761-0.56511.0534-0.730.8397-0.00840.12911.0152-0.07470.746193.2825126.006-71.4316
1075.77454.6956-5.28977.773-6.2686.0836-0.50022.094-0.6201-1.50070.43020.49391.5521-0.92210.02171.0111-0.2841-0.35752.0379-0.1891.1914252.061113.536727.5734
1082.3364-0.32872.71893.8283-3.40415.5772-1.1133-1.83720.27672.6750.7122-0.6937-0.807-0.00450.38891.2890.0285-0.19112.0105-0.02960.9469251.3709100.555842.3458
1093.482.883-3.13025.3509-2.14262.9157-0.3539-0.1726-0.14270.76950.1403-1.05890.19190.5690.231.131-0.17880.02991.4788-0.06611.1446246.401993.811237.5871
1106.49371.03740.37380.36880.06570.097-0.2215-1.97050.4461.28870.2549-0.6274-0.31640.4058-0.06731.0403-0.2056-0.19111.7475-0.08330.7434247.0647105.487429.5277
1116.4944-0.47110.80353.6193-1.10243.2317-0.042-1.1593-0.03240.5655-0.0417-0.47190.03040.42120.08491.0217-0.0622-0.10731.5883-0.08950.7821249.781396.981629.2129
1128.7625-5.04177.50972.9447-4.31696.4906-0.5905-0.0390.29370.25760.5544-0.3923-0.34420.61190.00651.0075-0.17310.08431.1133-0.08420.6704241.083297.690618.2002
1131.1865-1.24222.19151.815-1.79677.30280.13960.13640.0262-0.0331-0.08470.38150.7803-0.1078-0.05620.6683-0.13720.11630.42220.12120.7351108.025142.305-19.7006
1143.00665.33960.66129.50211.17230.14460.3812-0.8880.28930.8553-0.27050.0667-0.33170.2549-0.14170.7297-0.1117-0.0690.70340.14130.6101105.749752.0123-14.6604
1151.19381.65991.56073.87484.29224.9098-0.5580.29280.2002-0.87030.1945-0.3207-0.97241.08790.27330.6444-0.209-0.04560.66610.27480.9477103.271952.6896-31.163
1165.4621-6.3164-3.92489.35023.17374.21820.1540.0141-0.86320.2634-0.4261.53641.0127-2.2070.20040.8531-0.12770.06031.0608-0.00090.879692.758548.5405-38.8026
1172.8465-3.6762-0.72764.94691.14260.67230.1147-1.51390.24751.6977-0.2113-0.4139-0.101-0.23590.03990.8847-0.3727-0.01661.2043-0.28530.9571251.52124.68462.2598
1185.1647-5.60634.38726.3339-4.81973.7714-0.14460.11210.3504-0.21190.1207-0.9202-0.96320.98580.04730.8389-0.25080.17190.6797-0.21460.9333248.0418129.933.6142
1197.1803-6.685-1.59686.9223-0.53356.2239-0.7015-0.10790.87010.78210.2033-0.7616-1.3880.57020.38010.9357-0.2677-0.04081.419-0.60440.937254.0944133.44819.7097
1206.27675.9970.79269.9391.27625.99540.007-0.22690.68960.1977-0.17111.2777-0.5894-1.1910.1560.70640.1378-0.09791.1415-0.19711.2583192.5645103.8936-0.9075
1217.28390.0645-3.69618.01541.18652.26610.414-1.38860.40111.51580.175-2.14210.28662.0846-0.39930.8563-0.0006-0.1811.8454-0.41191.1511205.374795.53494.5308
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:920)
2X-RAY DIFFRACTION2chain 'A' and (resseq 921:1400)
3X-RAY DIFFRACTION3chain 'A' and (resseq 1401:1532)
4X-RAY DIFFRACTION4chain 'A' and (resseq 1533:1541)
5X-RAY DIFFRACTION5chain 'B' and (resseq 7:25)
6X-RAY DIFFRACTION6chain 'B' and (resseq 26:64)
7X-RAY DIFFRACTION7chain 'B' and (resseq 65:86)
8X-RAY DIFFRACTION8chain 'B' and (resseq 87:122)
9X-RAY DIFFRACTION9chain 'B' and (resseq 123:148)
10X-RAY DIFFRACTION10chain 'B' and (resseq 149:226)
11X-RAY DIFFRACTION11chain 'B' and (resseq 227:240)
12X-RAY DIFFRACTION12chain 'C' and (resseq 2:112)
13X-RAY DIFFRACTION13chain 'C' and (resseq 113:207)
14X-RAY DIFFRACTION14chain 'D' and (resseq 2:34)
15X-RAY DIFFRACTION15chain 'D' and (resseq 35:67)
16X-RAY DIFFRACTION16chain 'D' and (resseq 68:148)
17X-RAY DIFFRACTION17chain 'D' and (resseq 149:181)
18X-RAY DIFFRACTION18chain 'D' and (resseq 182:209)
19X-RAY DIFFRACTION19chain 'E' and (resseq 5:14)
20X-RAY DIFFRACTION20chain 'E' and (resseq 15:27)
21X-RAY DIFFRACTION21chain 'E' and (resseq 28:50)
22X-RAY DIFFRACTION22chain 'E' and (resseq 51:63)
23X-RAY DIFFRACTION23chain 'E' and (resseq 64:79)
24X-RAY DIFFRACTION24chain 'E' and (resseq 80:86)
25X-RAY DIFFRACTION25chain 'E' and (resseq 87:103)
26X-RAY DIFFRACTION26chain 'E' and (resseq 104:140)
27X-RAY DIFFRACTION27chain 'E' and (resseq 141:154)
28X-RAY DIFFRACTION28chain 'F' and (resseq 1:32)
29X-RAY DIFFRACTION29chain 'F' and (resseq 33:92)
30X-RAY DIFFRACTION30chain 'F' and (resseq 93:101)
31X-RAY DIFFRACTION31chain 'G' and (resseq 2:11)
32X-RAY DIFFRACTION32chain 'G' and (resseq 12:20)
33X-RAY DIFFRACTION33chain 'G' and (resseq 21:52)
34X-RAY DIFFRACTION34chain 'G' and (resseq 53:57)
35X-RAY DIFFRACTION35chain 'G' and (resseq 58:79)
36X-RAY DIFFRACTION36chain 'G' and (resseq 80:92)
37X-RAY DIFFRACTION37chain 'G' and (resseq 93:109)
38X-RAY DIFFRACTION38chain 'G' and (resseq 110:129)
39X-RAY DIFFRACTION39chain 'G' and (resseq 130:144)
40X-RAY DIFFRACTION40chain 'G' and (resseq 145:156)
41X-RAY DIFFRACTION41chain 'H' and (resseq 1:18)
42X-RAY DIFFRACTION42chain 'H' and (resseq 19:29)
43X-RAY DIFFRACTION43chain 'H' and (resseq 30:41)
44X-RAY DIFFRACTION44chain 'H' and (resseq 42:53)
45X-RAY DIFFRACTION45chain 'H' and (resseq 54:62)
46X-RAY DIFFRACTION46chain 'H' and (resseq 63:72)
47X-RAY DIFFRACTION47chain 'H' and (resseq 73:85)
48X-RAY DIFFRACTION48chain 'H' and (resseq 86:95)
49X-RAY DIFFRACTION49chain 'H' and (resseq 96:100)
50X-RAY DIFFRACTION50chain 'H' and (resseq 101:106)
51X-RAY DIFFRACTION51chain 'H' and (resseq 107:116)
52X-RAY DIFFRACTION52chain 'H' and (resseq 117:127)
53X-RAY DIFFRACTION53chain 'H' and (resseq 128:138)
54X-RAY DIFFRACTION54chain 'I' and (resseq 2:25)
55X-RAY DIFFRACTION55chain 'I' and (resseq 26:32)
56X-RAY DIFFRACTION56chain 'I' and (resseq 33:53)
57X-RAY DIFFRACTION57chain 'I' and (resseq 54:88)
58X-RAY DIFFRACTION58chain 'I' and (resseq 89:97)
59X-RAY DIFFRACTION59chain 'I' and (resseq 98:117)
60X-RAY DIFFRACTION60chain 'I' and (resseq 118:128)
61X-RAY DIFFRACTION61chain 'J' and (resseq 3:29)
62X-RAY DIFFRACTION62chain 'J' and (resseq 30:42)
63X-RAY DIFFRACTION63chain 'J' and (resseq 43:47)
64X-RAY DIFFRACTION64chain 'J' and (resseq 48:70)
65X-RAY DIFFRACTION65chain 'J' and (resseq 71:78)
66X-RAY DIFFRACTION66chain 'J' and (resseq 79:85)
67X-RAY DIFFRACTION67chain 'J' and (resseq 86:93)
68X-RAY DIFFRACTION68chain 'J' and (resseq 94:100)
69X-RAY DIFFRACTION69chain 'K' and (resseq 11:34)
70X-RAY DIFFRACTION70chain 'K' and (resseq 35:57)
71X-RAY DIFFRACTION71chain 'K' and (resseq 58:75)
72X-RAY DIFFRACTION72chain 'K' and (resseq 76:100)
73X-RAY DIFFRACTION73chain 'K' and (resseq 101:110)
74X-RAY DIFFRACTION74chain 'K' and (resseq 111:126)
75X-RAY DIFFRACTION75chain 'L' and (resseq 5:32)
76X-RAY DIFFRACTION76chain 'L' and (resseq 33:128)
77X-RAY DIFFRACTION77chain 'M' and (resseq 2:14)
78X-RAY DIFFRACTION78chain 'M' and (resseq 15:21)
79X-RAY DIFFRACTION79chain 'M' and (resseq 22:61)
80X-RAY DIFFRACTION80chain 'M' and (resseq 62:83)
81X-RAY DIFFRACTION81chain 'M' and (resseq 84:93)
82X-RAY DIFFRACTION82chain 'M' and (resseq 94:119)
83X-RAY DIFFRACTION83chain 'N' and (resseq 2:11)
84X-RAY DIFFRACTION84chain 'N' and (resseq 12:16)
85X-RAY DIFFRACTION85chain 'N' and (resseq 17:24)
86X-RAY DIFFRACTION86chain 'N' and (resseq 25:29)
87X-RAY DIFFRACTION87chain 'N' and (resseq 30:61)
88X-RAY DIFFRACTION88chain 'O' and (resseq 2:15)
89X-RAY DIFFRACTION89chain 'O' and (resseq 16:49)
90X-RAY DIFFRACTION90chain 'O' and (resseq 50:73)
91X-RAY DIFFRACTION91chain 'O' and (resseq 74:88)
92X-RAY DIFFRACTION92chain 'P' and (resseq 1:19)
93X-RAY DIFFRACTION93chain 'P' and (resseq 20:43)
94X-RAY DIFFRACTION94chain 'P' and (resseq 44:52)
95X-RAY DIFFRACTION95chain 'P' and (resseq 53:62)
96X-RAY DIFFRACTION96chain 'P' and (resseq 63:83)
97X-RAY DIFFRACTION97chain 'Q' and (resseq 2:17)
98X-RAY DIFFRACTION98chain 'Q' and (resseq 18:82)
99X-RAY DIFFRACTION99chain 'Q' and (resseq 83:100)
100X-RAY DIFFRACTION100chain 'R' and (resseq 19:23)
101X-RAY DIFFRACTION101chain 'R' and (resseq 24:28)
102X-RAY DIFFRACTION102chain 'R' and (resseq 29:36)
103X-RAY DIFFRACTION103chain 'R' and (resseq 37:43)
104X-RAY DIFFRACTION104chain 'R' and (resseq 44:52)
105X-RAY DIFFRACTION105chain 'R' and (resseq 53:76)
106X-RAY DIFFRACTION106chain 'R' and (resseq 77:88)
107X-RAY DIFFRACTION107chain 'S' and (resseq 2:12)
108X-RAY DIFFRACTION108chain 'S' and (resseq 13:25)
109X-RAY DIFFRACTION109chain 'S' and (resseq 26:35)
110X-RAY DIFFRACTION110chain 'S' and (resseq 36:40)
111X-RAY DIFFRACTION111chain 'S' and (resseq 41:70)
112X-RAY DIFFRACTION112chain 'S' and (resseq 71:81)
113X-RAY DIFFRACTION113chain 'T' and (resseq 8:66)
114X-RAY DIFFRACTION114chain 'T' and (resseq 67:75)
115X-RAY DIFFRACTION115chain 'T' and (resseq 76:91)
116X-RAY DIFFRACTION116chain 'T' and (resseq 92:106)
117X-RAY DIFFRACTION117chain 'U' and (resseq 2:8)
118X-RAY DIFFRACTION118chain 'U' and (resseq 9:15)
119X-RAY DIFFRACTION119chain 'U' and (resseq 16:25)
120X-RAY DIFFRACTION120chain 'a' and (resseq 1:6)
121X-RAY DIFFRACTION121chain 'b' and (resseq 30:40)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more