8RC9

W-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystallized with Formate and Exposed to air for 2 h

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
2.36	47.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.18	α = 90
b = 127.926	β = 90
c = 149.467	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		2022-07-06	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	2.06	97.19	87.87	0.991	7	4.3		65092

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	2.06	2.15			0.495

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	2.06	97.19	65087	3244	82.903	0.209	0.2064	0.2549	40.723

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]
0.21			-0.119		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.648
r_dihedral_angle_4_deg	17.496
r_dihedral_angle_3_deg	14.396
r_dihedral_angle_1_deg	7.287
r_lrange_it	6.163
r_lrange_other	6.156
r_mcangle_it	4.565
r_mcangle_other	4.565
r_scangle_it	4.373
r_scangle_other	4.372
r_mcbond_other	3.099
r_mcbond_it	3.098
r_scbond_it	2.898
r_scbond_other	2.888
r_angle_refined_deg	1.393
r_angle_other_deg	1.153
r_symmetry_xyhbond_nbd_refined	0.301
r_nbd_refined	0.194
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.16
r_nbd_other	0.152
r_xyhbond_nbd_refined	0.138
r_symmetry_nbd_refined	0.104
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.066
r_symmetry_xyhbond_nbd_other	0.012
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9230
Nucleic Acid Atoms
Solvent Atoms	207
Heterogen Atoms	150

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