9C0Q | pdb_00009c0q

Carbon monoxide dehydrogenase (CODH) from Methanosarcina thermophila, specimen prepared on blot plunger

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.727
f_angle_d	0.556
f_chiral_restr	0.042
f_plane_restr	0.004
f_bond_d	0.003

Sample
Acetyl-CoA decarbonylase/synthase complex

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	GATAN CRYOPLUNGE 3
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	99894
Reported Resolution (Å)	3.3
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C2

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol
Refinement Target	Correlation coefficient
Overall B Value	90.5204
Fitting Procedure
Details	Initial model was generated using AlphaFold, fit to the map using ChimeraX, followed by rigid body fitting in phenix, and finally iterative real space ...	Initial model was generated using AlphaFold, fit to the map using ChimeraX, followed by rigid body fitting in phenix, and finally iterative real space refinement in coot and phenix.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	54.53

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	2100
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	105000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	3.3.2
IMAGE ACQUISITION	EPU
MODEL FITTING	UCSF ChimeraX	1.6.1
MODEL FITTING	PHENIX	1.21.1_5286
MODEL FITTING	Coot	0.9.8.92
MODEL REFINEMENT	PHENIX	1.21.1_5286
INITIAL EULER ASSIGNMENT	cryoSPARC	3.3.2
FINAL EULER ASSIGNMENT	RELION	4.0
CLASSIFICATION	RELION	4.0
RECONSTRUCTION	RELION	4.0

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		852015

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.