8BQL

W-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystallized with Formate and Reoxidized by exposure to air for 12 min


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6SDV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829326% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl, 10 mM sodium formate
Crystal Properties
Matthews coefficientSolvent content
2.3247.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.8α = 90
b = 127.594β = 90
c = 148.622γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2022-07-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.9686ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.90696.99994.460.99679.08610.9582382
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9062.0080.62

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6SDV1.90696.99982370404585.0370.190.18780.225133.79
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]
0.147-0.1730.026
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.14
r_dihedral_angle_4_deg17.859
r_dihedral_angle_3_deg13.431
r_dihedral_angle_1_deg7.022
r_lrange_other6.624
r_lrange_it6.617
r_scangle_it5.259
r_scangle_other5.258
r_mcangle_it4.585
r_mcangle_other4.585
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.14
r_dihedral_angle_4_deg17.859
r_dihedral_angle_3_deg13.431
r_dihedral_angle_1_deg7.022
r_lrange_other6.624
r_lrange_it6.617
r_scangle_it5.259
r_scangle_other5.258
r_mcangle_it4.585
r_mcangle_other4.585
r_scbond_it3.592
r_scbond_other3.592
r_mcbond_it3.32
r_mcbond_other3.32
r_angle_refined_deg1.278
r_angle_other_deg1.154
r_nbd_refined0.189
r_symmetry_nbd_other0.176
r_nbd_other0.172
r_nbtor_refined0.159
r_xyhbond_nbd_refined0.134
r_symmetry_xyhbond_nbd_refined0.127
r_symmetry_nbd_refined0.115
r_symmetry_nbtor_other0.074
r_chiral_restr0.056
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9234
Nucleic Acid Atoms
Solvent Atoms373
Heterogen Atoms162

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata processing
STARANISOdata scaling
PHASERphasing
autoPROCdata reduction