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Macromolecular crystal data phased by negative staining electron microscopy reconstructions

by single particle reconstruction, at 15 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 165, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 165, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1680
TitleMacromolecular crystal data phased by negative staining electron microscopy reconstructions
MapMacromolecular crystal data phased by negative staining electron microscopy reconstructions as a proof of principle
SampleType-II dehydroquinase (DHQ) from Candida albicans (CaDHQ)
KeywordsNegative staining, electron microscopy, reconstructions, phasing
AuthorsTrapani S, Schoehn G, Navaza J, Abergel C
DateDeposition: 2010-01-13, Header release: 2010-01-18, Map release: 2011-01-28, Last update: 2012-08-29
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 165, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 165, Made by UCSF CHIMERA

Supplemental images

emd-1680.png
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
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Diagram

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Article
Citation - Primary
ArticleActa Crystallogr. D Biol. Crystallogr., Vol. 66, Issue Pt 5, Page 514-21, Year 2010
TitleMacromolecular crystal data phased by negative-stained electron-microscopy reconstructions.
AuthorsStefano Trapani, Guy Schoehn, Jorge Navaza, Chantal Abergel
Université de Montpellier 1, Montpellier, France.
Keywords3-dehydroquinate dehydratase (4.2.1.10), Candida albicans (enzymology), Crystallography, X-Ray (methods), Hydro-Lyases (chemistry, 4.2.1.-), Microscopy, Electron (methods)
LinksDOI: 10.1107/S0907444910002763, PubMed: 20445226
Map
FileEMD-1680.map ( map file in CCP4 format, 2636 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:165 (by emdb), 165 (movie #1):
Minimum - Maximum: -335 - 426.472
Average (Standard dev.): 31.2115 (113.128)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 87 87 87
Origin : 0 0 0
Limit : 86 86 86
Spacing : 87 87 87
Unit CellA = 121.8 A , B = 121.8 A , C = 121.8 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 1.4 A , Y = 1.4 A , Z = 1.4 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.41.41.4
M x/y/z878787
origin x/y/z0.0000.0000.000
length x/y/z121.800121.800121.800
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ121121121
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS878787
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-335.000426.47231.212
Annotation DetailsMacromolecular crystal data phased by negative staining electron microscopy reconstructions as a proof of principle
Supplement
Images
Images

emd-1680.png
Sample
NameType-II dehydroquinase (DHQ) from Candida albicans (CaDHQ)
Number of Components1
Oligomeric StateDodecamer
Experimental Mass0.2 MDa
Component #1: protein - CaDHQ
Scientific nameCaDHQ
Theoretical Mass0.017 MDa
Oligomeric DetailsDodecamer
Number of Copies12
Scientific Name of SpeciesCandida albicans (NCBI Taxonomy: 5476)
Recombinant expressionYes
Engineered SourceExp System: Escherichia coli (NCBI Taxonomy: 562)
Experiment
Sample Preparation
StainingNegative staining using 1% methylamine vanadate, CH3NH2VO3
Specimen Conc0.05 mg/ml
Specimen Support Details400 mesk copper grid
Specimen Stateparticle
BufferDetails: 20mM NaCl, 10mM Tris-HCL
pH: 7.4
Vitrification
Cryogen NameNONE
DetailsNegative staining at room temperature
InstrumentNONE
Imaging
MicroscopeJEOL 1200EXII
Date12-DEC-2006
DetailsLow dose negative staining
Electron Gun
Electron SourceTUNGSTEN HAIRPIN
Accelerating Voltage100 kV
Illumination ModeOTHER
Lens
MagnificationNominal: 50000 X,
AstigmatismObjective lens astigmatism was corrected at 100,000 times magnification
Imaging ModeBRIGHT FIELD
Defocus1000 nm - 2500 nm
Specimen Holder
HolderEucentric ( JEOL )
Camera
DetectorKodak SO163 film
Image Acquisition
ScannerZEISS SCAI
Number of Digital Images8
Sampling Size7 microns
Quant Bit Number8
Processing
Methodsingle particle reconstruction
3 D reconstruction
AlgorithmBack projection
SoftwareSpider
CTF CorrectionEach negative
Details7200 particles included in the reconstruction (out of 12000). 432 symmetry imposed
Resolution By Author15
Resolution MethodFSC at 0.5 cut off
Single Particle
Number of Class Averages114
Number of Projections7200
Download
Data from EMDB
Header (meta data in XML format)emd-1680.xml (7 KB)
Map dataemd_1680.map.gz (2 MB)
Imagesemd-1680.png (278.6 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1680
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 26 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 26.1 KB