9G7I | pdb_00009g7i

Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) in complex with acetyl-Coenyzme A from Clostridium autoethanogenum

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YTT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293.15	Crystallization was performed anaerobically by initial screening at 20 degrees Celsius using the sitting drop method on 96 Well MRC 2 Drop polystyrene Crystallization Plates SWISSCI in a Coy tent containing an N2/H2 (97:3%) atmosphere. The reservoir contained 90 ul of 25 % (w/v) glycerol ethoxylate 1,000, 100 mM Tris/HCl pH 8.5, and 100 mM CaCl2. 0.6 ul of crystallization solution was mixed with 0.6 ul of the protein, containing a final concentration of 2 mM acetyl-CoA. The protein was concentrated at 15 mg/ml in 25 mM Tris/HCl pH 7.6, 10% (v/v) glycerol, and 2 mM dithiothreitol. The crystals appeared in few weeks and were soaked in the crystallization solution supplemented with 15% (v/v) Ethylene glycol for a few seconds before freezing in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
4.74	74.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 298.077	α = 90
b = 298.077	β = 90
c = 127.526	γ = 90

Symmetry
Space Group	P 42 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 2M-F		2021-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00003	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.93	59.61	96.1	0.207	0.045	0.211	0.045	0.998	14.5	22.1		99666

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.93	3.16	73		2.423	0.513	2.477	0.513	0.593	1.6	23.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.93	49.68	1.33	99636	5002	81.39	0.1917	0.1902	0.1921	0.2202	0.2186	89.64

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.855
f_angle_d	1.367
f_chiral_restr	0.09
f_bond_d	0.01
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20122
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	342

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

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.