8BQI

W-formate dehydrogenase from Desulfovibrio vulgaris - Soaking with Formate 3 min


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829324% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties
Matthews coefficientSolvent content
2.2946.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.992α = 90
b = 123.751β = 90
c = 150.358γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 16M2022-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.8856ESRFID23-1

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
12.356150.3698.30.99294.849978
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)
12.3562.430.409

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-VALUE6SDR2.35695.73349943240997.970.2140.21280.247744.55
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]
0.82-1.8791.058
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.39
r_dihedral_angle_4_deg17.55
r_dihedral_angle_3_deg14.874
r_dihedral_angle_1_deg6.977
r_lrange_it5.247
r_lrange_other5.247
r_mcangle_it3.611
r_mcangle_other3.611
r_scangle_it3.499
r_scangle_other3.499
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.39
r_dihedral_angle_4_deg17.55
r_dihedral_angle_3_deg14.874
r_dihedral_angle_1_deg6.977
r_lrange_it5.247
r_lrange_other5.247
r_mcangle_it3.611
r_mcangle_other3.611
r_scangle_it3.499
r_scangle_other3.499
r_mcbond_it2.313
r_mcbond_other2.313
r_scbond_it2.19
r_scbond_other2.19
r_angle_refined_deg1.282
r_angle_other_deg1.097
r_symmetry_xyhbond_nbd_refined0.274
r_nbd_refined0.184
r_symmetry_nbd_other0.178
r_nbd_other0.173
r_nbtor_refined0.157
r_symmetry_nbd_refined0.148
r_xyhbond_nbd_refined0.147
r_symmetry_nbtor_other0.073
r_chiral_restr0.05
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9197
Nucleic Acid Atoms
Solvent Atoms65
Heterogen Atoms170

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata processing
PHASERphasing
autoPROCdata reduction
STARANISOdata scaling