8BQJ | pdb_00008bqj

W-formate dehydrogenase from Desulfovibrio vulgaris - Soaking with Formate 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
2.28	46.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.351	α = 90
b = 150.55	β = 90
c = 64.941	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	2.107	95.597	92.88	0.9941	9.051	4.33		45854

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	2.107	2.359			0.552

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	6SDR	2.107	95.597	45839	2296	64.818	0.215	0.2139	0.22	0.2449	0.25	38.776

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]
-0.555			-0.261		0.816

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.711
r_dihedral_angle_4_deg	15.979
r_dihedral_angle_3_deg	13.623
r_dihedral_angle_1_deg	6.848
r_lrange_it	4.235
r_lrange_other	4.235
r_mcangle_it	2.718
r_mcangle_other	2.718
r_scangle_it	2.53
r_scangle_other	2.53
r_mcbond_it	1.654
r_mcbond_other	1.654
r_scbond_it	1.515
r_scbond_other	1.515
r_angle_refined_deg	1.234
r_angle_other_deg	1.078
r_nbd_refined	0.18
r_symmetry_nbd_other	0.171
r_nbtor_refined	0.156
r_nbd_other	0.149
r_xyhbond_nbd_refined	0.139
r_symmetry_nbd_refined	0.118
r_symmetry_nbtor_other	0.071
r_chiral_restr	0.045
r_symmetry_xyhbond_nbd_other	0.019
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_symmetry_xyhbond_nbd_refined	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9197
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	155

Software

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