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W-formate dehydrogenase M405S from Desulfovibrio vulgaris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SDR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 32% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.22 44.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.341 α = 90 b = 127.226 β = 90 c = 148.266 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 X 9M 2023-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8731 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.005 48.592 93.02 0.996 7.381 4.61 71441
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.005 2.118 0.562
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.005 48.592 71375 3497 86.56 0.214 0.2124 0.2212 0.2528 0.2598 40.166
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.998 r_dihedral_angle_4_deg 20.091 r_dihedral_angle_3_deg 13.611 r_dihedral_angle_1_deg 7.069 r_lrange_it 4.961 r_lrange_other 4.952 r_mcangle_it 3.071 r_mcangle_other 3.071 r_scangle_other 2.849 r_scangle_it 2.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.998 r_dihedral_angle_4_deg 20.091 r_dihedral_angle_3_deg 13.611 r_dihedral_angle_1_deg 7.069 r_lrange_it 4.961 r_lrange_other 4.952 r_mcangle_it 3.071 r_mcangle_other 3.071 r_scangle_other 2.849 r_scangle_it 2.847 r_mcbond_it 1.919 r_mcbond_other 1.919 r_scbond_it 1.739 r_scbond_other 1.736 r_angle_refined_deg 1.313 r_angle_other_deg 1.142 r_nbd_refined 0.191 r_nbd_other 0.183 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.141 r_symmetry_nbtor_other 0.073 r_symmetry_nbd_refined 0.056 r_chiral_restr 0.054 r_symmetry_xyhbond_nbd_other 0.048 r_symmetry_xyhbond_nbd_refined 0.039 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9197 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 163
Software Software Software Name Purpose REFMAC refinement STARANISO data scaling PHASER phasing XDS data reduction