8BQK

W-formate dehydrogenase from Desulfovibrio vulgaris - Soaking with Formate 22 min


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829322% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties
Matthews coefficientSolvent content
2.2645.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.684α = 90
b = 123.874β = 90
c = 149.181γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 16M2021-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.7749ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.58795.48492.250.0770.998211.3364.681299786
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)
11.5871.70.5794

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-VALUE6SDR1.58795.484129786650980.0020.1710.16950.192328.477
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]
-0.035-0.1460.181
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.178
r_dihedral_angle_4_deg17.968
r_dihedral_angle_3_deg12.899
r_dihedral_angle_1_deg7.09
r_lrange_it6.794
r_lrange_other6.781
r_scangle_it5.745
r_scangle_other5.745
r_scbond_it4.099
r_scbond_other4.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.178
r_dihedral_angle_4_deg17.968
r_dihedral_angle_3_deg12.899
r_dihedral_angle_1_deg7.09
r_lrange_it6.794
r_lrange_other6.781
r_scangle_it5.745
r_scangle_other5.745
r_scbond_it4.099
r_scbond_other4.098
r_mcangle_other3.971
r_mcangle_it3.97
r_mcbond_it3.087
r_mcbond_other3.086
r_angle_refined_deg1.387
r_angle_other_deg1.297
r_nbd_other0.215
r_nbd_refined0.203
r_symmetry_nbd_other0.18
r_nbtor_refined0.164
r_symmetry_nbd_refined0.162
r_symmetry_xyhbond_nbd_other0.125
r_xyhbond_nbd_refined0.116
r_symmetry_xyhbond_nbd_refined0.103
r_symmetry_nbtor_other0.077
r_chiral_restr0.076
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9211
Nucleic Acid Atoms
Solvent Atoms458
Heterogen Atoms192

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata processing
STARANISOdata scaling
PHASERphasing
autoPROCdata reduction