8RCG

W-formate dehydrogenase M405S 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 DROP829332% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties
Matthews coefficientSolvent content
2.2244.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.341α = 90
b = 127.226β = 90
c = 148.266γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 9M2023-02-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.8731ESRFID30B

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
12.00548.59293.020.9967.3814.6171441
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)
12.0052.1180.562

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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-VALUE2.00548.59271375349786.560.2140.21240.252840.166
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]
0.244-0.068-0.176
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.998
r_dihedral_angle_4_deg20.091
r_dihedral_angle_3_deg13.611
r_dihedral_angle_1_deg7.069
r_lrange_it4.961
r_lrange_other4.952
r_mcangle_it3.071
r_mcangle_other3.071
r_scangle_other2.849
r_scangle_it2.847
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.998
r_dihedral_angle_4_deg20.091
r_dihedral_angle_3_deg13.611
r_dihedral_angle_1_deg7.069
r_lrange_it4.961
r_lrange_other4.952
r_mcangle_it3.071
r_mcangle_other3.071
r_scangle_other2.849
r_scangle_it2.847
r_mcbond_it1.919
r_mcbond_other1.919
r_scbond_it1.739
r_scbond_other1.736
r_angle_refined_deg1.313
r_angle_other_deg1.142
r_nbd_refined0.191
r_nbd_other0.183
r_symmetry_nbd_other0.182
r_nbtor_refined0.16
r_xyhbond_nbd_refined0.141
r_symmetry_nbtor_other0.073
r_symmetry_nbd_refined0.056
r_chiral_restr0.054
r_symmetry_xyhbond_nbd_other0.048
r_symmetry_xyhbond_nbd_refined0.039
r_bond_refined_d0.005
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 Atoms9197
Nucleic Acid Atoms
Solvent Atoms244
Heterogen Atoms163

Software

Software
Software NamePurpose
REFMACrefinement
STARANISOdata scaling
PHASERphasing
XDSdata reduction