8RCB | pdb_00008rcb

W-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystallized with Formate and Reoxidized by exposure to air (in a not degassed drop) for 34 min in the presence of Formate

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

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.433	α = 90
b = 123.085	β = 90
c = 148.138	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	2.11	94.67	91.15	0.996	8.4	8.9		54097

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	2.11	2.28			0.591

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6SDV	2.11	94.67	54095	2723	78.843	0.201	0.1991	0.21	0.2404	0.25	38.678

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]
0.269			-0.3		0.031

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.644
r_dihedral_angle_4_deg	15.849
r_dihedral_angle_3_deg	13.162
r_lrange_it	8.759
r_lrange_other	8.758
r_scangle_it	7.166
r_scangle_other	7.166
r_dihedral_angle_1_deg	6.725
r_mcangle_it	6.409
r_mcangle_other	6.409
r_scbond_it	5.062
r_scbond_other	5.062
r_mcbond_other	4.789
r_mcbond_it	4.788
r_angle_refined_deg	1.212
r_angle_other_deg	1.072
r_nbd_refined	0.176
r_symmetry_nbd_other	0.169
r_nbd_other	0.163
r_symmetry_nbd_refined	0.162
r_nbtor_refined	0.155
r_xyhbond_nbd_refined	0.125
r_symmetry_xyhbond_nbd_refined	0.086
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.045
r_symmetry_xyhbond_nbd_other	0.011
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9159
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	157

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