8BQJ

W-formate dehydrogenase from Desulfovibrio vulgaris - Soaking with Formate 5 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
2.2846.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.351α = 90
b = 150.55β = 90
c = 64.941γ = 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
12.10795.59792.880.99419.0514.3345854
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)
12.1072.3590.552

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-VALUE6SDR2.10795.59745839229664.8180.2150.21390.244938.776
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]
-0.555-0.2610.816
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.711
r_dihedral_angle_4_deg15.979
r_dihedral_angle_3_deg13.623
r_dihedral_angle_1_deg6.848
r_lrange_it4.235
r_lrange_other4.235
r_mcangle_it2.718
r_mcangle_other2.718
r_scangle_it2.53
r_scangle_other2.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.711
r_dihedral_angle_4_deg15.979
r_dihedral_angle_3_deg13.623
r_dihedral_angle_1_deg6.848
r_lrange_it4.235
r_lrange_other4.235
r_mcangle_it2.718
r_mcangle_other2.718
r_scangle_it2.53
r_scangle_other2.53
r_mcbond_it1.654
r_mcbond_other1.654
r_scbond_it1.515
r_scbond_other1.515
r_angle_refined_deg1.234
r_angle_other_deg1.078
r_nbd_refined0.18
r_symmetry_nbd_other0.171
r_nbtor_refined0.156
r_nbd_other0.149
r_xyhbond_nbd_refined0.139
r_symmetry_nbd_refined0.118
r_symmetry_nbtor_other0.071
r_chiral_restr0.045
r_symmetry_xyhbond_nbd_other0.019
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_symmetry_xyhbond_nbd_refined0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9197
Nucleic Acid Atoms
Solvent Atoms79
Heterogen Atoms155

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata processing
STARANISOdata scaling
PHASERphasing
autoPROCdata reduction