8RC8

W-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystallized with Formate and Exposed to air for 0 min


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829322% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties
Matthews coefficientSolvent content
2.2244.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.988α = 90
b = 124.345β = 90
c = 149.899γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2022-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.9686ESRFID30B

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
1247.89899.60.9946.6782099
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)
122.040.527

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-VALUE6SDV2.00547.89882000415299.7060.1830.18110.219531.242
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]
0.796-1.280.484
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.145
r_dihedral_angle_3_deg12.971
r_dihedral_angle_1_deg6.724
r_lrange_it6.5
r_lrange_other6.424
r_dihedral_angle_2_deg5.388
r_scangle_it4.774
r_scangle_other4.773
r_mcangle_it3.969
r_mcangle_other3.968
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.145
r_dihedral_angle_3_deg12.971
r_dihedral_angle_1_deg6.724
r_lrange_it6.5
r_lrange_other6.424
r_dihedral_angle_2_deg5.388
r_scangle_it4.774
r_scangle_other4.773
r_mcangle_it3.969
r_mcangle_other3.968
r_scbond_it3.286
r_scbond_other3.286
r_mcbond_it2.873
r_mcbond_other2.872
r_angle_refined_deg1.052
r_angle_other_deg0.362
r_symmetry_nbd_refined0.243
r_nbd_other0.208
r_nbd_refined0.2
r_symmetry_nbd_other0.186
r_nbtor_refined0.171
r_symmetry_xyhbond_nbd_refined0.151
r_xyhbond_nbd_refined0.124
r_metal_ion_refined0.081
r_symmetry_nbtor_other0.075
r_chiral_restr0.058
r_bond_refined_d0.004
r_gen_planes_refined0.004
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 Atoms422
Heterogen Atoms171

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata processing
Aimlessdata scaling
PHASERphasing
XDSdata reduction
Aimlessdata scaling
XSCALEdata scaling
pointlessdata scaling