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W-formate dehydrogenase U192C from Desulfovibrio vulgaris - Soaked with Dithionite
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 26% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.04 39.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.8 α = 90 b = 122.511 β = 90 c = 146.697 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 EIGER R 4M 2021-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
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 1.997 62.93 99.57 0.994 9.3 7 76000
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 1.997 2.03 0.682
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 1.997 62.93 76000 3696 99.534 0.216 0.2139 0.2214 0.2672 0.2723 31.133
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] 1.038 -0.928 -0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.53 r_dihedral_angle_4_deg 18.189 r_lrange_other 14.945 r_lrange_it 14.919 r_dihedral_angle_3_deg 14.718 r_scangle_other 13.572 r_scangle_it 13.529 r_mcangle_it 12.663 r_mcangle_other 12.662 r_scbond_other 12.259
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.53 r_dihedral_angle_4_deg 18.189 r_lrange_other 14.945 r_lrange_it 14.919 r_dihedral_angle_3_deg 14.718 r_scangle_other 13.572 r_scangle_it 13.529 r_mcangle_it 12.663 r_mcangle_other 12.662 r_scbond_other 12.259 r_scbond_it 12.202 r_mcbond_it 11.859 r_mcbond_other 11.859 r_dihedral_angle_1_deg 6.813 r_angle_refined_deg 1.238 r_angle_other_deg 1.079 r_nbd_refined 0.176 r_symmetry_nbd_other 0.172 r_nbd_other 0.164 r_nbtor_refined 0.156 r_xyhbond_nbd_refined 0.136 r_symmetry_xyhbond_nbd_refined 0.122 r_symmetry_nbd_refined 0.073 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.047 r_symmetry_xyhbond_nbd_other 0.046 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9235 Nucleic Acid Atoms Solvent Atoms 415 Heterogen Atoms 170
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing