8RC8

W-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystallized with Formate and Exposed to air for 0 min

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6SDV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	22% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.988	α = 90
b = 124.345	β = 90
c = 149.899	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 PILATUS3 6M		2022-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.9686	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	47.898	99.6	0.994	6.6	7		82099

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	2.04			0.527

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	6SDV	2.005	47.898	82000	4152	99.706	0.183	0.1811	0.2195	31.242

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]
0.796			-1.28		0.484

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.145
r_dihedral_angle_3_deg	12.971
r_dihedral_angle_1_deg	6.724
r_lrange_it	6.5
r_lrange_other	6.424
r_dihedral_angle_2_deg	5.388
r_scangle_it	4.774
r_scangle_other	4.773
r_mcangle_it	3.969
r_mcangle_other	3.968
r_scbond_it	3.286
r_scbond_other	3.286
r_mcbond_it	2.873
r_mcbond_other	2.872
r_angle_refined_deg	1.052
r_angle_other_deg	0.362
r_symmetry_nbd_refined	0.243
r_nbd_other	0.208
r_nbd_refined	0.2
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.151
r_xyhbond_nbd_refined	0.124
r_metal_ion_refined	0.081
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.058
r_bond_refined_d	0.004
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	9211
Nucleic Acid Atoms
Solvent Atoms	422
Heterogen Atoms	171

Software

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