7Z5O | pdb_00007z5o

W-formate dehydrogenase from Desulfovibrio vulgaris - Dithionite reduced form

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.811	α = 90
b = 124.15	β = 90
c = 149.666	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 PILATUS 6M		2020-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.9793	ALBA	XALOC

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	1.527	95.737	99.6	0.997	9.8	4.5		182484

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	1.527	1.553			0.591

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6sdv	1.527	95.737	182475	9121	99.583	0.121	0.1192	0.12	0.1529	0.15	23.874

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]
-0.234			-0.28		0.514

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.114
r_dihedral_angle_4_deg	18.767
r_dihedral_angle_3_deg	12.224
r_dihedral_angle_1_deg	6.743
r_mcbond_it	2.079
r_mcbond_other	2.078
r_angle_refined_deg	1.415
r_angle_other_deg	1.389
r_nbd_other	0.237
r_nbd_refined	0.207
r_symmetry_nbd_refined	0.186
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.122
r_symmetry_xyhbond_nbd_refined	0.114
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.08
r_symmetry_xyhbond_nbd_other	0.041
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9211
Nucleic Acid Atoms
Solvent Atoms	722
Heterogen Atoms	191

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
PHASER	phasing