7Z5O

W-formate dehydrogenase from Desulfovibrio vulgaris - Dithionite reduced form


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION829326% PEG 3350, 0.1 M Tris-HCl pH 8.0 and 1 M LiCl
Crystal Properties
Matthews coefficientSolvent content
2.346.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.811α = 90
b = 124.15β = 90
c = 149.666γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.9793ALBAXALOC

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
11.52795.73799.60.9979.84.5182484
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)
11.5271.5530.591

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-VALUE6sdv1.52795.737182475912199.5830.1210.11920.152923.874
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]
-0.234-0.280.514
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.114
r_dihedral_angle_4_deg18.767
r_dihedral_angle_3_deg12.224
r_dihedral_angle_1_deg6.743
r_mcbond_it2.079
r_mcbond_other2.078
r_angle_refined_deg1.415
r_angle_other_deg1.389
r_nbd_other0.237
r_nbd_refined0.207
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.114
r_dihedral_angle_4_deg18.767
r_dihedral_angle_3_deg12.224
r_dihedral_angle_1_deg6.743
r_mcbond_it2.079
r_mcbond_other2.078
r_angle_refined_deg1.415
r_angle_other_deg1.389
r_nbd_other0.237
r_nbd_refined0.207
r_symmetry_nbd_refined0.186
r_symmetry_nbd_other0.179
r_nbtor_refined0.166
r_xyhbond_nbd_refined0.122
r_symmetry_xyhbond_nbd_refined0.114
r_chiral_restr0.083
r_symmetry_nbtor_other0.08
r_symmetry_xyhbond_nbd_other0.041
r_bond_refined_d0.007
r_gen_planes_refined0.007
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 Atoms722
Heterogen Atoms191

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata processing
PHASERphasing