4AB2 | pdb_00004ab2

ATP-triggered molecular mechanics of the chaperonin GroEL

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OEL

Sample
GROEL-ATP14 RD2-RD4

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK I
Cryogen Name	ETHANE
Sample Vitrification Details	VITRIFIED WITH A VITROBOT AT 100 PERCENT HUMIDITY WITH 2-3 SECONDS BLOTTING TIME

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	6500
Reported Resolution (Å)	8.5
Resolution Method
Other Details	CHAINS A-G ARE IN THE RD4 ATP BOUND CONFORMATION. CHAINS H-N ARE IN THE RD2 ATP BOUND CONFORMATION SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2002. (DEPOSITION ID: 10411).
Refinement Type
Symmetry Type	POINT
Point Symmetry	D7

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

Data Acquisition
Detector Type	GATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å**2)	15

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)	95
Microscope Model	FEI TECNAI F20
Minimum Defocus (nm)	700
Maximum Defocus (nm)	3500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification	148500
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	120
Imaging Details	THE DATA WERE COLLECTED WITH LEGINON AT SCRIPPS

EM Software
Task	Software Package	Version
MODEL FITTING	Flex-EM
MODEL FITTING	NAMD	2.6
MODEL FITTING	UCSF Chimera
RECONSTRUCTION	IMAGIC
RECONSTRUCTION	SPIDER

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	EACH PARTICLE WAS PHASE FLIPPED