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W-formate dehydrogenase U192C 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 34% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.07 40.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.396 α = 90 b = 123.099 β = 90 c = 147.189 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 1.833 63.167 92.92 0.9884 5.959 4.83 74505
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 1.833 2.006 0.668
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 1.833 63.167 74504 3891 74.387 0.175 0.1723 0.1825 0.2135 0.2173 25.248
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] 0.215 -0.08 -0.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.108 r_dihedral_angle_4_deg 18.579 r_dihedral_angle_3_deg 13.677 r_dihedral_angle_1_deg 6.888 r_lrange_it 6.771 r_lrange_other 6.762 r_scangle_other 5.793 r_scangle_it 5.776 r_scbond_other 4.197 r_mcangle_it 4.194
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.108 r_dihedral_angle_4_deg 18.579 r_dihedral_angle_3_deg 13.677 r_dihedral_angle_1_deg 6.888 r_lrange_it 6.771 r_lrange_other 6.762 r_scangle_other 5.793 r_scangle_it 5.776 r_scbond_other 4.197 r_mcangle_it 4.194 r_mcangle_other 4.194 r_scbond_it 4.18 r_mcbond_it 3.225 r_mcbond_other 3.222 r_angle_refined_deg 1.262 r_angle_other_deg 1.146 r_symmetry_xyhbond_nbd_refined 0.208 r_nbd_refined 0.186 r_nbd_other 0.176 r_symmetry_nbd_other 0.174 r_nbtor_refined 0.158 r_symmetry_nbd_refined 0.14 r_symmetry_xyhbond_nbd_other 0.128 r_xyhbond_nbd_refined 0.126 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.056 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9256 Nucleic Acid Atoms Solvent Atoms 431 Heterogen Atoms 245
Software Software Software Name Purpose REFMAC refinement autoPROC data processing STARANISO data scaling PHASER phasing XDS data reduction Aimless data scaling XSCALE data scaling pointless data scaling