8BQG

W-formate dehydrogenase from Desulfovibrio vulgaris - Soaking with Formate 1 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
2.2444.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.537α = 90
b = 122.778β = 90
c = 148.985γ = 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
11.94694.9391.960.99719.24.3373334
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)
11.952.070.435

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-VALUE6SDR1.94694.9373316356483.6570.1950.19290.242738.302
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]
0.093-0.1660.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.87
r_dihedral_angle_4_deg20.114
r_dihedral_angle_3_deg15.847
r_dihedral_angle_1_deg7.601
r_lrange_it6.551
r_lrange_other6.551
r_scangle_it5.158
r_scangle_other5.158
r_mcangle_it4.392
r_mcangle_other4.392
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.87
r_dihedral_angle_4_deg20.114
r_dihedral_angle_3_deg15.847
r_dihedral_angle_1_deg7.601
r_lrange_it6.551
r_lrange_other6.551
r_scangle_it5.158
r_scangle_other5.158
r_mcangle_it4.392
r_mcangle_other4.392
r_scbond_it3.535
r_scbond_other3.535
r_mcbond_it3.229
r_mcbond_other3.229
r_angle_refined_deg1.618
r_angle_other_deg1.278
r_nbd_other0.22
r_nbd_refined0.202
r_symmetry_nbd_other0.19
r_nbtor_refined0.168
r_xyhbond_nbd_refined0.165
r_symmetry_nbd_refined0.159
r_chiral_restr0.084
r_symmetry_nbtor_other0.08
r_symmetry_xyhbond_nbd_other0.047
r_symmetry_xyhbond_nbd_refined0.034
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9197
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms164

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata processing
STARANISOdata scaling
PHASERphasing
autoPROCdata reduction