8CM7

W-formate dehydrogenase M405A from Desulfovibrio vulgaris


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829330% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties
Matthews coefficientSolvent content
2.3146.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.874α = 90
b = 123.833β = 90
c = 149.891γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2022-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.9677ESRFMASSIF-3

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
12.11775.05892.30.9948.316.947566
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)
12.1172.2980.613

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-VALUE6SDR2.11775.05847565241768.3560.20.1970.251838.585
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]
-0.4480.0160.433
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.371
r_dihedral_angle_4_deg17.924
r_dihedral_angle_3_deg15.223
r_dihedral_angle_1_deg7.583
r_lrange_it6.417
r_lrange_other6.409
r_scangle_it4.47
r_scangle_other4.47
r_mcangle_it4.239
r_mcangle_other4.239
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.371
r_dihedral_angle_4_deg17.924
r_dihedral_angle_3_deg15.223
r_dihedral_angle_1_deg7.583
r_lrange_it6.417
r_lrange_other6.409
r_scangle_it4.47
r_scangle_other4.47
r_mcangle_it4.239
r_mcangle_other4.239
r_scbond_it2.903
r_scbond_other2.902
r_mcbond_it2.817
r_mcbond_other2.817
r_angle_refined_deg1.547
r_angle_other_deg1.216
r_symmetry_xyhbond_nbd_refined0.87
r_nbd_other0.231
r_nbd_refined0.203
r_symmetry_nbd_other0.19
r_nbtor_refined0.166
r_xyhbond_nbd_refined0.152
r_symmetry_nbd_refined0.151
r_symmetry_xyhbond_nbd_other0.094
r_symmetry_nbtor_other0.079
r_chiral_restr0.075
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9149
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms185

Software

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