8RCG

W-formate dehydrogenase M405S from 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	32% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.341	α = 90
b = 127.226	β = 90
c = 148.266	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 EIGER2 X 9M		2023-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.8731	ESRF	ID30B

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	2.005	48.592	93.02	0.996	7.381	4.61		71441

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	2.005	2.118			0.562

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.005	48.592	71375	3497	86.56	0.214	0.2124	0.2528	40.166

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]
0.244			-0.068		-0.176

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.998
r_dihedral_angle_4_deg	20.091
r_dihedral_angle_3_deg	13.611
r_dihedral_angle_1_deg	7.069
r_lrange_it	4.961
r_lrange_other	4.952
r_mcangle_it	3.071
r_mcangle_other	3.071
r_scangle_other	2.849
r_scangle_it	2.847
r_mcbond_it	1.919
r_mcbond_other	1.919
r_scbond_it	1.739
r_scbond_other	1.736
r_angle_refined_deg	1.313
r_angle_other_deg	1.142
r_nbd_refined	0.191
r_nbd_other	0.183
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.141
r_symmetry_nbtor_other	0.073
r_symmetry_nbd_refined	0.056
r_chiral_restr	0.054
r_symmetry_xyhbond_nbd_other	0.048
r_symmetry_xyhbond_nbd_refined	0.039
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9197
Nucleic Acid Atoms
Solvent Atoms	244
Heterogen Atoms	163

Software

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