9RK1 | pdb_00009rk1

W-formate dehydrogenase W491E from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris)

X-RAY DIFFRACTION

---

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	30% 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 = 64.824	α = 90
b = 128.043	β = 90
c = 148.748	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		2025-05-12	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	1.993	74.374	93.2	0.9874	7.12	6.98		69547

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	1.993	2.146			0.5072

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	1.993	74.374	69547	3530	81.553	0.211	0.2086	0.217	0.2582	0.2624	35.311

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]
0.137			-0.09		-0.047

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.641
r_dihedral_angle_4_deg	19.658
r_dihedral_angle_3_deg	12.914
r_lrange_it	7.484
r_lrange_other	7.484
r_dihedral_angle_1_deg	6.521
r_scangle_it	5.69
r_scangle_other	5.689
r_mcangle_it	5.678
r_mcangle_other	5.678
r_mcbond_it	4.032
r_mcbond_other	4.031
r_scbond_it	3.964
r_scbond_other	3.963
r_angle_refined_deg	1.225
r_angle_other_deg	1.068
r_nbd_other	0.177
r_nbd_refined	0.172
r_symmetry_nbd_other	0.168
r_symmetry_nbd_refined	0.159
r_nbtor_refined	0.153
r_xyhbond_nbd_refined	0.126
r_symmetry_xyhbond_nbd_refined	0.105
r_symmetry_nbtor_other	0.071
r_chiral_restr	0.045
r_bond_refined_d	0.003
r_gen_planes_refined	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	9230
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms	150

Software

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