3I01 | pdb_00003i01

Native structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase from Moorella thermoacetica, water-bound C-cluster.

X-RAY DIFFRACTION

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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	7.6	298	8% PEG MME 5000, 20% glycerol, 200 mM calcium acetate, 100 mM Pipes, pH 6.5, 2 mM dithiothreitol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.651	α = 101.26
b = 136.87	β = 109.11
c = 140.864	γ = 104.08

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	MARMOSAIC 325 mm CCD		2003-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.95469	SSRL	BL11-1

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	2.15	36.96	92.3	0.067		2.1	310437	326694

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	2.15	2.21	90.4		0.46	2.3	2.1

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	Rigid body refinement from previously solved structure	THROUGHOUT	PDB entry 1MJG	2.15	36.96	310437	16243	92.3	0.18902	0.18627	0.19	0.24154	0.24	RANDOM	36.935

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]
-1.09	0.15	-0.47	0.2	-1.27	0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.533
r_dihedral_angle_4_deg	21.299
r_dihedral_angle_3_deg	18.396
r_dihedral_angle_1_deg	7.141
r_scangle_it	4.248
r_scbond_it	2.818
r_angle_refined_deg	1.871
r_mcangle_it	1.648
r_mcbond_it	0.954
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.25
r_nbd_refined	0.228
r_symmetry_hbond_refined	0.179
r_xyhbond_nbd_refined	0.172
r_metal_ion_refined	0.151
r_chiral_restr	0.134
r_bond_refined_d	0.021
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	43306
Nucleic Acid Atoms
Solvent Atoms	1413
Heterogen Atoms	164

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling