2VDC

THE 9.5 A RESOLUTION STRUCTURE OF GLUTAMATE SYNTHASE FROM CRYO-ELECTRON MICROSCOPY AND ITS OLIGOMERIZATION BEHAVIOR IN SOLUTION: FUNCTIONAL IMPLICATIONS.


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VDC 
Sample
AZOSPIRILLUM BRASILENSE GLUTAMATE SYNTHASE
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification DetailsNLIQUID ETHANE
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles12800
Reported Resolution (Å)9.5
Resolution Method
Other DetailsTHE CHAINS A,B,C,D,E,F OF THE COMPLEX CORRESPOND TO THE ALPHA SUBUNITS, SOLVED BY X-RAY (PDB CODE 1EA0). THREE DISORDERED REGIONS OF THIS X-RAY STRUCT ...THE CHAINS A,B,C,D,E,F OF THE COMPLEX CORRESPOND TO THE ALPHA SUBUNITS, SOLVED BY X-RAY (PDB CODE 1EA0). THREE DISORDERED REGIONS OF THIS X-RAY STRUCTURE (CHAINS A,B,C,D,E, F), IE RESIDUES 305-307, 1172-1179 AND 1194-1202 WERE MODELLED WITH MODELLER. THE CHAINS G,H,I,J,K,L CORRESPOND TO THE HOMOLOGY MODEL OF THE BETA SUBUNIT (GENERATED BY MODELLER).
Refinement Type
Symmetry TypePOINT
Point SymmetryI
Map-Model Fitting and Refinement
Id1 (2VDC)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsMETHOD--REAL-SPACE LOCAL OPTIMIZATION REFINEMENT PROTOCOL--X-RAY AND HOMOLOGY MODELLING
Data Acquisition
Detector TypeKODAK SO-163 FILM
Electron Dose (electrons/Å**2)10
Imaging Experiment1
Date of Experiment2005-05-10
Temperature (Kelvin)93.15
Microscope ModelJEOL 2010UHR
Minimum Defocus (nm)1700
Maximum Defocus (nm)3200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS0.5
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification50000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging DetailsCC =1.1 MM, FOCAL -LEN-1.9 M. MICROGRAPH WITH ANISOTROPIC OR NO DIFFRACTION RINGS WERE REMOVED USING THE ENHANCED POWER SPECTRA SORTING METHOD (JONIC S,SORZANO CO,COTTEVIEILLE M, LARQUET E, BOISSET N.,A NOVEL METHOD FOR IMPROVEMENT OF VISUALIZATION OF POWER SPECTRA FOR SORTING CRYO-ELECTRON MICROGRAPHS AND THEIR LOCAL AREAS. J STRUCT BIOL. 2007, 157(1),156-67.)
EM Software
TaskSoftware PackageVersion
MODEL FITTINGUCSF Chimera
RECONSTRUCTIONSPIDER
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
WIENER FILTERING OF VOLUMES FROM FOCAL SERIES