9QM1 | pdb_00009qm1

W-formate dehydrogenase U192C from Desulfovibrio vulgaris - Soaked with Dithionite

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	26% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.8	α = 90
b = 122.511	β = 90
c = 146.697	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER R 4M		2021-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.997	62.93	99.57	0.994	9.3	7		76000

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.997	2.03			0.682

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.997	62.93	76000	3696	99.534	0.216	0.2139	0.2214	0.2672	0.2723	31.133

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]
1.038			-0.928		-0.111

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.53
r_dihedral_angle_4_deg	18.189
r_lrange_other	14.945
r_lrange_it	14.919
r_dihedral_angle_3_deg	14.718
r_scangle_other	13.572
r_scangle_it	13.529
r_mcangle_it	12.663
r_mcangle_other	12.662
r_scbond_other	12.259
r_scbond_it	12.202
r_mcbond_it	11.859
r_mcbond_other	11.859
r_dihedral_angle_1_deg	6.813
r_angle_refined_deg	1.238
r_angle_other_deg	1.079
r_nbd_refined	0.176
r_symmetry_nbd_other	0.172
r_nbd_other	0.164
r_nbtor_refined	0.156
r_xyhbond_nbd_refined	0.136
r_symmetry_xyhbond_nbd_refined	0.122
r_symmetry_nbd_refined	0.073
r_symmetry_nbtor_other	0.071
r_chiral_restr	0.047
r_symmetry_xyhbond_nbd_other	0.046
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9235
Nucleic Acid Atoms
Solvent Atoms	415
Heterogen Atoms	170

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing