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W-formate dehydrogenase S194A from Nitratidesulfovibrio vulgaris (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 28% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.2 44.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.696 α = 90 b = 123.84 β = 90 c = 149.714 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 2024-06-23 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 2.24 95.425 99.67 0.9826 4.697 5.07 58277
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 2.24 2.28 0.3038
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 2.243 95.425 58111 2868 99.388 0.218 0.2161 0.2266 0.252 0.2621 37.455
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] -0.439 -0.095 0.534
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.205 r_dihedral_angle_4_deg 17.602 r_dihedral_angle_3_deg 14.098 r_dihedral_angle_1_deg 6.93 r_lrange_it 2.647 r_lrange_other 2.645 r_mcangle_it 1.445 r_mcangle_other 1.445 r_angle_refined_deg 1.262 r_scangle_it 1.162
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.205 r_dihedral_angle_4_deg 17.602 r_dihedral_angle_3_deg 14.098 r_dihedral_angle_1_deg 6.93 r_lrange_it 2.647 r_lrange_other 2.645 r_mcangle_it 1.445 r_mcangle_other 1.445 r_angle_refined_deg 1.262 r_scangle_it 1.162 r_scangle_other 1.162 r_angle_other_deg 1.084 r_mcbond_it 0.816 r_mcbond_other 0.816 r_scbond_it 0.65 r_scbond_other 0.65 r_nbd_refined 0.179 r_symmetry_nbd_other 0.174 r_symmetry_nbd_refined 0.174 r_nbd_other 0.173 r_nbtor_refined 0.155 r_xyhbond_nbd_refined 0.137 r_symmetry_nbtor_other 0.073 r_symmetry_xyhbond_nbd_refined 0.069 r_chiral_restr 0.049 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 9196 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement autoPROC data processing PHASER phasing XDS data reduction Aimless data scaling XSCALE data scaling pointless data scaling