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- PDB-7m2t: Crystallographic Structure of the Monoclinic Form of Satellite To... -

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Basic information

Entry
Database: PDB / ID: 7m2t
TitleCrystallographic Structure of the Monoclinic Form of Satellite Tobacco Mosaic Virus
Components
  • Coat protein
  • RNA (27-mer)
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
KeywordsVIRUS/RNA / VIRUS-RNA complex
Function / homologySatellite virus coat domain superfamily / viral capsid / structural molecule activity / PHOSPHATE ION / RNA / RNA (> 10) / Coat protein
Function and homology information
Biological speciesSatellite tobacco mosaic virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsMcPherson, A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Structures of additional crystal forms of Satellite tobacco mosaic virus grown from a variety of salts.
Authors: McPherson, A.
History
DepositionMar 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Q: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
R: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
S: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
T: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
U: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
V: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
W: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
X: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Y: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Z: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
a: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
b: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
c: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
d: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
e: RNA (27-mer)
f: RNA (27-mer)
g: RNA (27-mer)
h: RNA (27-mer)
i: RNA (27-mer)
j: RNA (27-mer)
k: RNA (27-mer)
l: RNA (27-mer)
m: RNA (27-mer)
n: RNA (27-mer)
o: RNA (27-mer)
p: RNA (27-mer)
q: RNA (27-mer)
r: RNA (27-mer)
s: RNA (27-mer)
t: RNA (27-mer)
u: RNA (27-mer)
v: RNA (27-mer)
w: RNA (27-mer)
x: RNA (27-mer)
y: RNA (27-mer)
z: RNA (27-mer)
1: RNA (27-mer)
2: RNA (27-mer)
3: RNA (27-mer)
4: RNA (27-mer)
5: RNA (27-mer)
6: RNA (27-mer)
7: RNA (27-mer)
8: RNA (27-mer)
BB: Coat protein
CC: Coat protein
DD: Coat protein
EE: Coat protein
FF: Coat protein
GG: Coat protein
HH: Coat protein
II: Coat protein
JJ: Coat protein
KK: Coat protein
LL: Coat protein
MM: Coat protein
NN: Coat protein
OO: Coat protein
PP: Coat protein
QQ: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
RR: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
SS: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
TT: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
UU: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
VV: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
WW: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
YY: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
ZZ: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
bb: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
cc: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
dd: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
ee: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
ff: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
gg: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
hh: RNA (27-mer)
ii: RNA (27-mer)
jj: RNA (27-mer)
kk: RNA (27-mer)
ll: RNA (27-mer)
mm: RNA (27-mer)
nn: RNA (27-mer)
oo: RNA (27-mer)
pp: RNA (27-mer)
qq: RNA (27-mer)
rr: RNA (27-mer)
ss: RNA (27-mer)
tt: RNA (27-mer)
uu: RNA (27-mer)
vv: RNA (27-mer)
ww: RNA (27-mer)
xx: RNA (27-mer)
yy: RNA (27-mer)
zz: RNA (27-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,047,234126
Polymers1,046,038109
Non-polymers1,19617
Water50,3882797
1
A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Q: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
R: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
S: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
T: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
U: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
V: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
W: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
X: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Y: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Z: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
a: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
b: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
c: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
d: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
e: RNA (27-mer)
f: RNA (27-mer)
g: RNA (27-mer)
h: RNA (27-mer)
i: RNA (27-mer)
j: RNA (27-mer)
k: RNA (27-mer)
l: RNA (27-mer)
m: RNA (27-mer)
n: RNA (27-mer)
o: RNA (27-mer)
p: RNA (27-mer)
q: RNA (27-mer)
r: RNA (27-mer)
s: RNA (27-mer)
t: RNA (27-mer)
u: RNA (27-mer)
v: RNA (27-mer)
w: RNA (27-mer)
x: RNA (27-mer)
y: RNA (27-mer)
z: RNA (27-mer)
1: RNA (27-mer)
2: RNA (27-mer)
3: RNA (27-mer)
4: RNA (27-mer)
5: RNA (27-mer)
6: RNA (27-mer)
7: RNA (27-mer)
8: RNA (27-mer)
BB: Coat protein
CC: Coat protein
DD: Coat protein
EE: Coat protein
FF: Coat protein
GG: Coat protein
HH: Coat protein
II: Coat protein
JJ: Coat protein
KK: Coat protein
LL: Coat protein
MM: Coat protein
NN: Coat protein
OO: Coat protein
PP: Coat protein
QQ: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
RR: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
SS: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
TT: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
UU: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
VV: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
WW: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
YY: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
ZZ: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
bb: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
cc: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
dd: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
ee: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
ff: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
gg: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
hh: RNA (27-mer)
ii: RNA (27-mer)
jj: RNA (27-mer)
kk: RNA (27-mer)
ll: RNA (27-mer)
mm: RNA (27-mer)
nn: RNA (27-mer)
oo: RNA (27-mer)
pp: RNA (27-mer)
qq: RNA (27-mer)
rr: RNA (27-mer)
ss: RNA (27-mer)
tt: RNA (27-mer)
uu: RNA (27-mer)
vv: RNA (27-mer)
ww: RNA (27-mer)
xx: RNA (27-mer)
yy: RNA (27-mer)
zz: RNA (27-mer)
hetero molecules

A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Q: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
R: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
S: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
T: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
U: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
V: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
W: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
X: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Y: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Z: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
a: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
b: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
c: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
d: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
e: RNA (27-mer)
f: RNA (27-mer)
g: RNA (27-mer)
h: RNA (27-mer)
i: RNA (27-mer)
j: RNA (27-mer)
k: RNA (27-mer)
l: RNA (27-mer)
m: RNA (27-mer)
n: RNA (27-mer)
o: RNA (27-mer)
p: RNA (27-mer)
q: RNA (27-mer)
r: RNA (27-mer)
s: RNA (27-mer)
t: RNA (27-mer)
u: RNA (27-mer)
v: RNA (27-mer)
w: RNA (27-mer)
x: RNA (27-mer)
y: RNA (27-mer)
z: RNA (27-mer)
1: RNA (27-mer)
2: RNA (27-mer)
3: RNA (27-mer)
4: RNA (27-mer)
5: RNA (27-mer)
6: RNA (27-mer)
7: RNA (27-mer)
8: RNA (27-mer)
BB: Coat protein
CC: Coat protein
DD: Coat protein
EE: Coat protein
FF: Coat protein
GG: Coat protein
HH: Coat protein
II: Coat protein
JJ: Coat protein
KK: Coat protein
LL: Coat protein
MM: Coat protein
NN: Coat protein
OO: Coat protein
PP: Coat protein
QQ: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
RR: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
SS: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
TT: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
UU: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
VV: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
WW: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
YY: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
ZZ: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
bb: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
cc: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
dd: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
ee: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
ff: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
gg: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
hh: RNA (27-mer)
ii: RNA (27-mer)
jj: RNA (27-mer)
kk: RNA (27-mer)
ll: RNA (27-mer)
mm: RNA (27-mer)
nn: RNA (27-mer)
oo: RNA (27-mer)
pp: RNA (27-mer)
qq: RNA (27-mer)
rr: RNA (27-mer)
ss: RNA (27-mer)
tt: RNA (27-mer)
uu: RNA (27-mer)
vv: RNA (27-mer)
ww: RNA (27-mer)
xx: RNA (27-mer)
yy: RNA (27-mer)
zz: RNA (27-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,094,469252
Polymers2,092,077218
Non-polymers2,39234
Water2,882160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)175.760, 169.860, 244.560
Angle α, β, γ (deg.)90.000, 92.690, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11Q-165-

A

21B-211-

HOH

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Components

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Protein , 1 types, 30 molecules ABCDEFGHIJKLMNOBBCCDDEEFFGGHHIIJJKKLLMMNNOOPP

#1: Protein ...
Coat protein


Mass: 17533.949 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Satellite tobacco mosaic virus / References: UniProt: P17574

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RNA chain , 2 types, 79 molecules PQRSTUVWXYZabcdQQRRSSTTUUVVWWYYZZbbccddeeffgg...

#2: RNA chain ...
RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 3905.512 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Details: arbitrary RNA adenine nucleotide dodecamer / Source: (natural) Satellite tobacco mosaic virus
#3: RNA chain ...
RNA (27-mer)


Mass: 8221.520 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Details: arbitrary RNA uridine nucleotide 27-mer / Source: (natural) Satellite tobacco mosaic virus

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Non-polymers , 4 types, 2814 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2797 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.74 Å3/Da / Density % sol: 29.43 %
Description: Thick, vertex truncated triangles of about 0.25 mm thickness and up to 1 mm across the faces.
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystals grown by vapor diffusion as sitting drops. Drops were equal volumes of a 6 mg/ml STMV stock solution buffered at pH 6.5 with 0.1 M phosphate. The reservoirs were 16% saturated ...Details: Crystals grown by vapor diffusion as sitting drops. Drops were equal volumes of a 6 mg/ml STMV stock solution buffered at pH 6.5 with 0.1 M phosphate. The reservoirs were 16% saturated ammonium sulfate in 0.1 M phosphate at pH 6.5. Drops were 6 to 8 ul with 0.60 ml reservoirs. Crystals were grown at 4 degrees C over a weeks time.
PH range: 4.5 - 7.0

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Jun 15, 1992
RadiationMonochromator: Supper graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→49.95 Å / Num. obs: 179156 / % possible obs: 91.8 % / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Biso Wilson estimate: 20.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0691 / Rpim(I) all: 0.036 / Rsym value: 0.0675 / Net I/σ(I): 9.27
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 5.7 / Num. unique obs: 11858 / Rsym value: 0.127 / % possible all: 58.8

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
SDMSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OQ8

4oq8


Resolution: 2.71→49.95 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 16.19 / Stereochemistry target values: ML
Details: Structure was refined extensively in REFMAC from CCP4 and then refined further using REFINE from PHENIX.
RfactorNum. reflection% reflection
Rfree0.1767 8864 4.95 %
Rwork0.1292 170271 -
obs0.1316 179135 91.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 269.82 Å2 / Biso mean: 25.2683 Å2 / Biso min: 6.28 Å2
Refinement stepCycle: final / Resolution: 2.71→49.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33540 13353 157 2797 49847
Biso mean--62.66 23.93 -
Num. residues----4975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00349297
X-RAY DIFFRACTIONf_angle_d0.52969991
X-RAY DIFFRACTIONf_chiral_restr0.0428628
X-RAY DIFFRACTIONf_plane_restr0.0066734
X-RAY DIFFRACTIONf_dihedral_angle_d10.51619815
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.71-2.740.2543730.19271654172727
2.74-2.770.29472400.19834469470973
2.77-2.80.2613010.17885294559586
2.8-2.840.21522800.15395400568086
2.84-2.870.22942760.14985348562487
2.87-2.910.23272760.13455389566588
2.91-2.960.192650.13035404566988
2.96-30.17772370.13065472570988
3-3.050.21262620.14775578584089
3.05-3.10.21542390.15915590582989
3.1-3.150.20712920.15425489578190
3.15-3.210.2112460.14295610585690
3.21-3.270.18962850.13055597588291
3.27-3.340.18792510.12585575582691
3.34-3.410.20593100.1195759606994
3.41-3.490.18573350.11956117645299
3.49-3.570.17582800.1156154643499
3.57-3.670.16843000.111962416541100
3.67-3.780.16693530.107561126465100
3.78-3.90.14064140.095460596473100
3.9-4.040.13093230.09461636486100
4.04-4.20.13733710.100561416512100
4.2-4.390.13712770.105462616538100
4.39-4.620.12783420.092361426484100
4.62-4.910.11032770.094962186495100
4.91-5.290.14663660.108561836549100
5.29-5.820.1663530.140861926545100
5.82-6.660.21362790.171262476526100
6.67-8.390.19473270.168962516578100
8.39-46.950.21044340.21566162659699
Refinement TLS params.Method: refined / Origin x: 22.387 Å / Origin y: -0.0064 Å / Origin z: 15.9798 Å
111213212223313233
T0.0661 Å20.0011 Å2-0.0004 Å2-0.0693 Å20.0001 Å2--0.0618 Å2
L0.0201 °20.0013 °20.0114 °2-0.0368 °2-0.0005 °2--0.029 °2
S0.0045 Å °-0.001 Å °-0.0041 Å °0.0068 Å °-0.0042 Å °-0.0142 Å °-0.0024 Å °0.0053 Å °0.0039 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA16 - 159
2X-RAY DIFFRACTION1allA201 - 525
3X-RAY DIFFRACTION1allB16 - 159
4X-RAY DIFFRACTION1allB201 - 405
5X-RAY DIFFRACTION1allC16 - 159
6X-RAY DIFFRACTION1allC201 - 503
7X-RAY DIFFRACTION1allD16 - 159
8X-RAY DIFFRACTION1allD201 - 405
9X-RAY DIFFRACTION1allE16 - 159
10X-RAY DIFFRACTION1allE201 - 500
11X-RAY DIFFRACTION1allF16 - 159
12X-RAY DIFFRACTION1allF201 - 509
13X-RAY DIFFRACTION1allG16 - 159
14X-RAY DIFFRACTION1allG201 - 406
15X-RAY DIFFRACTION1allH16 - 159
16X-RAY DIFFRACTION1allH201 - 515
17X-RAY DIFFRACTION1allI16 - 159
18X-RAY DIFFRACTION1allI202 - 416
19X-RAY DIFFRACTION1allJ16 - 159
20X-RAY DIFFRACTION1allJ203 - 412
21X-RAY DIFFRACTION1allK16 - 159
22X-RAY DIFFRACTION1allK201 - 491
23X-RAY DIFFRACTION1allL16 - 159
24X-RAY DIFFRACTION1allL201 - 420
25X-RAY DIFFRACTION1allM16 - 159
26X-RAY DIFFRACTION1allM201 - 399
27X-RAY DIFFRACTION1allN16 - 159
28X-RAY DIFFRACTION1allN202 - 406
29X-RAY DIFFRACTION1allO16 - 159
30X-RAY DIFFRACTION1allO201 - 409
31X-RAY DIFFRACTION1allP161 - 170
32X-RAY DIFFRACTION1allP207
33X-RAY DIFFRACTION1allQ161 - 170
34X-RAY DIFFRACTION1allQ201 - 212
35X-RAY DIFFRACTION1allR161 - 170
36X-RAY DIFFRACTION1allR206 - 208
37X-RAY DIFFRACTION1allS161 - 170
38X-RAY DIFFRACTION1allS203 - 211
39X-RAY DIFFRACTION1allT161 - 170
40X-RAY DIFFRACTION1allU161 - 170
41X-RAY DIFFRACTION1allV161 - 170
42X-RAY DIFFRACTION1allV210 - 212
43X-RAY DIFFRACTION1allW161 - 170
44X-RAY DIFFRACTION1allW208 - 210
45X-RAY DIFFRACTION1allX161 - 170
46X-RAY DIFFRACTION1allY161 - 170
47X-RAY DIFFRACTION1allY201 - 206
48X-RAY DIFFRACTION1allZ161 - 170
49X-RAY DIFFRACTION1allZ201 - 209
50X-RAY DIFFRACTION1alla161 - 170
51X-RAY DIFFRACTION1alla210 - 211
52X-RAY DIFFRACTION1allb161 - 170
53X-RAY DIFFRACTION1allb201 - 210
54X-RAY DIFFRACTION1allc161 - 170
55X-RAY DIFFRACTION1allc203 - 207
56X-RAY DIFFRACTION1alld161 - 170
57X-RAY DIFFRACTION1alld202 - 204
58X-RAY DIFFRACTION1alle181 - 190
59X-RAY DIFFRACTION1alle205 - 207
60X-RAY DIFFRACTION1allf181 - 190
61X-RAY DIFFRACTION1allg181 - 190
62X-RAY DIFFRACTION1allh181 - 190
63X-RAY DIFFRACTION1alli181 - 190
64X-RAY DIFFRACTION1alli204 - 209
65X-RAY DIFFRACTION1allj181 - 190
66X-RAY DIFFRACTION1allj201 - 204
67X-RAY DIFFRACTION1allk181 - 190
68X-RAY DIFFRACTION1alll181 - 190
69X-RAY DIFFRACTION1allm181 - 190
70X-RAY DIFFRACTION1alln181 - 190
71X-RAY DIFFRACTION1alln203
72X-RAY DIFFRACTION1allo181 - 190
73X-RAY DIFFRACTION1allo204 - 205
74X-RAY DIFFRACTION1allp181 - 190
75X-RAY DIFFRACTION1allq181 - 190
76X-RAY DIFFRACTION1allr181 - 190
77X-RAY DIFFRACTION1allr201
78X-RAY DIFFRACTION1alls181 - 190
79X-RAY DIFFRACTION1alls202 - 205
80X-RAY DIFFRACTION1allt195 - 196
81X-RAY DIFFRACTION1allt201
82X-RAY DIFFRACTION1allu195 - 196
83X-RAY DIFFRACTION1allv195 - 196
84X-RAY DIFFRACTION1allw195 - 196
85X-RAY DIFFRACTION1allx195 - 196
86X-RAY DIFFRACTION1ally195 - 196
87X-RAY DIFFRACTION1allz195 - 196
88X-RAY DIFFRACTION1all1195 - 196
89X-RAY DIFFRACTION1all2195 - 196
90X-RAY DIFFRACTION1all3195 - 196
91X-RAY DIFFRACTION1all4195 - 196
92X-RAY DIFFRACTION1all5195 - 196
93X-RAY DIFFRACTION1all6195 - 196
94X-RAY DIFFRACTION1all7195 - 216
95X-RAY DIFFRACTION1all8195 - 196
96X-RAY DIFFRACTION1allBB16 - 159
97X-RAY DIFFRACTION1allBB201 - 525
98X-RAY DIFFRACTION1allCC16 - 159
99X-RAY DIFFRACTION1allCC201 - 406
100X-RAY DIFFRACTION1allDD16 - 159
101X-RAY DIFFRACTION1allDD201 - 504
102X-RAY DIFFRACTION1allEE16 - 159
103X-RAY DIFFRACTION1allEE201 - 403
104X-RAY DIFFRACTION1allFF16 - 159
105X-RAY DIFFRACTION1allFF201 - 501
106X-RAY DIFFRACTION1allGG16 - 159
107X-RAY DIFFRACTION1allGG201 - 512
108X-RAY DIFFRACTION1allHH16 - 159
109X-RAY DIFFRACTION1allHH201 - 379
110X-RAY DIFFRACTION1allII16 - 159
111X-RAY DIFFRACTION1allII201 - 515
112X-RAY DIFFRACTION1allJJ16 - 159
113X-RAY DIFFRACTION1allJJ201 - 415
114X-RAY DIFFRACTION1allKK16 - 159
115X-RAY DIFFRACTION1allKK201 - 410
116X-RAY DIFFRACTION1allLL16 - 159
117X-RAY DIFFRACTION1allLL201 - 493
118X-RAY DIFFRACTION1allMM16 - 159
119X-RAY DIFFRACTION1allMM201 - 426
120X-RAY DIFFRACTION1allNN16 - 159
121X-RAY DIFFRACTION1allNN201 - 397
122X-RAY DIFFRACTION1allOO16 - 159
123X-RAY DIFFRACTION1allOO202 - 410
124X-RAY DIFFRACTION1allPP16 - 159
125X-RAY DIFFRACTION1allPP201 - 408
126X-RAY DIFFRACTION1allQQ161 - 170
127X-RAY DIFFRACTION1allQQ202
128X-RAY DIFFRACTION1allRR161 - 170
129X-RAY DIFFRACTION1allRR206 - 207
130X-RAY DIFFRACTION1allSS161 - 170
131X-RAY DIFFRACTION1allSS206 - 208
132X-RAY DIFFRACTION1allTT161 - 170
133X-RAY DIFFRACTION1allTT209 - 211
134X-RAY DIFFRACTION1allUU161 - 170
135X-RAY DIFFRACTION1allVV161 - 170
136X-RAY DIFFRACTION1allWW161 - 170
137X-RAY DIFFRACTION1allWW201 - 212
138X-RAY DIFFRACTION1allYY161 - 170
139X-RAY DIFFRACTION1allZZ161 - 170
140X-RAY DIFFRACTION1allbb161 - 170
141X-RAY DIFFRACTION1allcc161 - 170
142X-RAY DIFFRACTION1alldd161 - 170
143X-RAY DIFFRACTION1allee161 - 170
144X-RAY DIFFRACTION1allff161 - 170
145X-RAY DIFFRACTION1allgg161 - 170
146X-RAY DIFFRACTION1allhh181 - 190
147X-RAY DIFFRACTION1allii181 - 190
148X-RAY DIFFRACTION1alljj181 - 190
149X-RAY DIFFRACTION1allkk181 - 190
150X-RAY DIFFRACTION1allll181 - 190
151X-RAY DIFFRACTION1allmm181 - 190
152X-RAY DIFFRACTION1allnn181 - 190
153X-RAY DIFFRACTION1alloo181 - 190
154X-RAY DIFFRACTION1allpp181 - 190
155X-RAY DIFFRACTION1allqq181 - 190
156X-RAY DIFFRACTION1allrr181 - 190
157X-RAY DIFFRACTION1allss184 - 190
158X-RAY DIFFRACTION1alltt181 - 190
159X-RAY DIFFRACTION1alluu181 - 190
160X-RAY DIFFRACTION1allvv181 - 190
161X-RAY DIFFRACTION1allww195 - 196
162X-RAY DIFFRACTION1allxx195 - 196
163X-RAY DIFFRACTION1allyy195 - 196
164X-RAY DIFFRACTION1allzz195 - 196
165X-RAY DIFFRACTION1allKK1 - 61

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