5FM1 | pdb_00005fm1

Structure of gamma-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure

ELECTRON MICROSCOPY

Sample
GAMMA TUBULIN SMALL COMPLEX

Specimen Preparation
Sample Aggregation State	FILAMENT
Vitrification Instrument	FEI VITROBOT MARK I
Cryogen Name	ETHANE
Sample Vitrification Details	LIQUID ETHANE

3D Reconstruction
Reconstruction Method	HELICAL
Number of Particles
Reported Resolution (Å)	8
Resolution Method
Other Details	INITIAL MODELS WERE GENERATED WITH MODELER 9.15 BASED ON PDB ENTRIES 3RIP (FOR GCP2 AND GCP3) AND 3CB2 (FOR GAMMA TUBULIN). TWO COMPLETE GAMMA-TUSC ST ...	INITIAL MODELS WERE GENERATED WITH MODELER 9.15 BASED ON PDB ENTRIES 3RIP (FOR GCP2 AND GCP3) AND 3CB2 (FOR GAMMA TUBULIN). TWO COMPLETE GAMMA-TUSC STRUCTURES WERE MODELED SIMULTANEOUSLY, RIGIDLY FITTED INTO THE CRYO-EM MAP WITH UCSF CHIMERA, THEN FLEXIBLY FITTED WITH MDFF. ADDITIONAL SECONDARY STRUCTURE AND SYMMETRY RESTRAINTS WERE ADDED. FINAL VALIDATION PERFORMED WITH THE INTEGRATIVE MODELING PLATFORM. FOR DETAILS, ALL CODE IS DEPOSITED AT GITHUB. COMSLASHINTEGRATIVEMODELINGSLASHGAMMA-TUSC SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1731. (DEPOSITION ID: 7273).
Refinement Type
Symmetry Type	HELICAL

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	METHOD--FLEXIBLE FITTING REFINEMENT PROTOCOL--X-RAY

Data Acquisition
Detector Type	TVIPS TEMCAM-F816 (8k x 8k)
Electron Dose (electrons/Å**2)	20

Imaging Experiment	1
Date of Experiment	2009-09-23
Temperature (Kelvin)
Microscope Model	FEI TECNAI F20
Minimum Defocus (nm)	800
Maximum Defocus (nm)	3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	60000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	IMP
MODEL FITTING	MDFF
MODEL FITTING	MODELLER
RECONSTRUCTION	SPIDER

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	WHOLE MICROGRAPH

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.