2Z8Y | pdb_00002z8y

Xenon-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase(CODH/ACS) from Moorella thermoacetica

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	8-10% (w/v) polyethylene glycol monomethyl ether 5000, 20% glycerol, 200mM calcium acetate, 100mM PIPES pH 6.5, 2mM dithiothreitol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.54	α = 101.29
b = 136.6	β = 109.22
c = 141.75	γ = 103.91

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4		2002-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.9184	SSRL	BL9-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	2.51	49	96.1	0.083	10.3	2.1	217468	217468			43.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.51	2.6	92		0.422	2	2	20805

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1MJG	2.51	49	203798	10717	96.1	0.182	0.178	0.18	0.25	RANDOM	31.3

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]
-1.03	0.21	-0.63	1.21	-0.59	-0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.475
r_dihedral_angle_4_deg	23.256
r_dihedral_angle_3_deg	20.786
r_dihedral_angle_1_deg	7.521
r_scangle_it	4.814
r_scbond_it	3.197
r_angle_refined_deg	2.284
r_mcangle_it	1.908
r_mcbond_it	1.075
r_nbtor_refined	0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.475
r_dihedral_angle_4_deg	23.256
r_dihedral_angle_3_deg	20.786
r_dihedral_angle_1_deg	7.521
r_scangle_it	4.814
r_scbond_it	3.197
r_angle_refined_deg	2.284
r_mcangle_it	1.908
r_mcbond_it	1.075
r_nbtor_refined	0.33
r_nbd_refined	0.251
r_symmetry_vdw_refined	0.231
r_metal_ion_refined	0.227
r_symmetry_hbond_refined	0.198
r_xyhbond_nbd_refined	0.171
r_chiral_restr	0.144
r_bond_refined_d	0.026
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	43321
Nucleic Acid Atoms
Solvent Atoms	1153
Heterogen Atoms	228

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	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.