8CM7

W-formate dehydrogenase M405A 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	30% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.874	α = 90
b = 123.833	β = 90
c = 149.891	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 X 4M		2022-02-16	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	2.117	75.058	92.3	0.994	8.31	6.9		47566

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	2.117	2.298			0.613

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6SDR	2.117	75.058	47565	2417	68.356	0.2	0.197	0.2518	38.585

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]
-0.448			0.016		0.433

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.371
r_dihedral_angle_4_deg	17.924
r_dihedral_angle_3_deg	15.223
r_dihedral_angle_1_deg	7.583
r_lrange_it	6.417
r_lrange_other	6.409
r_scangle_it	4.47
r_scangle_other	4.47
r_mcangle_it	4.239
r_mcangle_other	4.239
r_scbond_it	2.903
r_scbond_other	2.902
r_mcbond_it	2.817
r_mcbond_other	2.817
r_angle_refined_deg	1.547
r_angle_other_deg	1.216
r_symmetry_xyhbond_nbd_refined	0.87
r_nbd_other	0.231
r_nbd_refined	0.203
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.152
r_symmetry_nbd_refined	0.151
r_symmetry_xyhbond_nbd_other	0.094
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9149
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	185

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