9RK0 | pdb_00009rk0

W-formate dehydrogenase S194A from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris)

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	28% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.696	α = 90
b = 123.84	β = 90
c = 149.714	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		2024-06-23	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	2.24	95.425	99.67	0.9826	4.697	5.07		58277

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	2.24	2.28			0.3038

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	2.243	95.425	58111	2868	99.388	0.218	0.2161	0.2266	0.252	0.2621	37.455

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]
-0.439			-0.095		0.534

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.205
r_dihedral_angle_4_deg	17.602
r_dihedral_angle_3_deg	14.098
r_dihedral_angle_1_deg	6.93
r_lrange_it	2.647
r_lrange_other	2.645
r_mcangle_it	1.445
r_mcangle_other	1.445
r_angle_refined_deg	1.262
r_scangle_it	1.162
r_scangle_other	1.162
r_angle_other_deg	1.084
r_mcbond_it	0.816
r_mcbond_other	0.816
r_scbond_it	0.65
r_scbond_other	0.65
r_nbd_refined	0.179
r_symmetry_nbd_other	0.174
r_symmetry_nbd_refined	0.174
r_nbd_other	0.173
r_nbtor_refined	0.155
r_xyhbond_nbd_refined	0.137
r_symmetry_nbtor_other	0.073
r_symmetry_xyhbond_nbd_refined	0.069
r_chiral_restr	0.049
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9196
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms	212

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
PHASER	phasing
XDS	data reduction
Aimless	data scaling
XSCALE	data scaling
pointless	data scaling