8BQK

W-formate dehydrogenase from Desulfovibrio vulgaris - Soaking with Formate 22 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	22% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.684	α = 90
b = 123.874	β = 90
c = 149.181	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		2021-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.7749	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.587	95.484	92.25	0.077	0.9982	11.336	4.68		1299786

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	1.587	1.7			0.5794

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	1.587	95.484	129786	6509	80.002	0.171	0.1695	0.1923	28.477

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]
-0.035			-0.146		0.181

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.178
r_dihedral_angle_4_deg	17.968
r_dihedral_angle_3_deg	12.899
r_dihedral_angle_1_deg	7.09
r_lrange_it	6.794
r_lrange_other	6.781
r_scangle_it	5.745
r_scangle_other	5.745
r_scbond_it	4.099
r_scbond_other	4.098
r_mcangle_other	3.971
r_mcangle_it	3.97
r_mcbond_it	3.087
r_mcbond_other	3.086
r_angle_refined_deg	1.387
r_angle_other_deg	1.297
r_nbd_other	0.215
r_nbd_refined	0.203
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.164
r_symmetry_nbd_refined	0.162
r_symmetry_xyhbond_nbd_other	0.125
r_xyhbond_nbd_refined	0.116
r_symmetry_xyhbond_nbd_refined	0.103
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.076
r_bond_refined_d	0.007
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	9211
Nucleic Acid Atoms
Solvent Atoms	458
Heterogen Atoms	192

Software

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