8CM5

W-formate dehydrogenase C872A 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	8CM4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	20% PEG 3350 (w/v), 0.1 M Tris-HCl pH 8.5 and 0.2 M CaCl2

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.44	α = 90
b = 261.055	β = 90.576
c = 126.209	γ = 90

Symmetry
Space Group	P 1 21 1

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		2021-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.9763	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	2.15	48.831	96.8	0.998	6.7	2.3		248226

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	2.15	2.19			0.453

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	2.15	48.831	248196	12240	96.766	0.187	0.184	0.2396	34.843

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]
-0.199		-1.52	0.418		-0.189

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.847
r_dihedral_angle_4_deg	18.391
r_dihedral_angle_3_deg	15.213
r_dihedral_angle_1_deg	7.818
r_lrange_it	6.56
r_lrange_other	6.557
r_scangle_other	4.914
r_scangle_it	4.911
r_mcangle_it	4.559
r_mcangle_other	4.559
r_scbond_other	3.217
r_scbond_it	3.215
r_mcbond_it	3.102
r_mcbond_other	3.102
r_angle_refined_deg	1.67
r_angle_other_deg	1.255
r_nbd_refined	0.206
r_nbd_other	0.191
r_symmetry_nbd_other	0.186
r_symmetry_xyhbond_nbd_refined	0.182
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.165
r_symmetry_nbd_refined	0.162
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.078
r_symmetry_xyhbond_nbd_other	0.04
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	37154
Nucleic Acid Atoms
Solvent Atoms	963
Heterogen Atoms	560

Software

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