8BQH

W-formate dehydrogenase from Desulfovibrio vulgaris - Soaking with Formate 1.5 min

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	24% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl

Crystal Properties
Matthews coefficient	Solvent content
2	38.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.361	α = 90
b = 127.456	β = 90
c = 128.952	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 S 16M		2022-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.8856	ESRF	ID23-1

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	1.61	90.65	94.14	0.996	9.5	5.7		94816

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	1.61	1.78			0.6555

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	1.61	90.65	94816	4778	68.517	0.152	0.1509	0.1754	19.364

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]
0.132			-0.062		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.373
r_dihedral_angle_4_deg	19.159
r_dihedral_angle_3_deg	13.409
r_lrange_it	7.282
r_lrange_other	7.264
r_dihedral_angle_1_deg	6.894
r_scangle_it	6.18
r_scangle_other	6.18
r_scbond_other	4.572
r_scbond_it	4.56
r_mcangle_it	3.913
r_mcangle_other	3.913
r_mcbond_other	2.927
r_mcbond_it	2.926
r_angle_refined_deg	1.601
r_angle_other_deg	1.452
r_symmetry_xyhbond_nbd_refined	0.286
r_nbd_other	0.213
r_nbd_refined	0.211
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.146
r_symmetry_nbd_refined	0.142
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9126
Nucleic Acid Atoms
Solvent Atoms	557
Heterogen Atoms	230

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
STARANISO	data scaling
PHASER	phasing
autoPROC	data reduction