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W-formate dehydrogenase from Desulfovibrio vulgaris - Soaking with Formate 5 min
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 24% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.28 46.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.351 α = 90 b = 150.55 β = 90 c = 64.941 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 S 16M 2022-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
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 2.107 95.597 92.88 0.9941 9.051 4.33 45854
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 2.107 2.359 0.552
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6SDR 2.107 95.597 45839 2296 64.818 0.215 0.2139 0.2207 0.2449 0.2517 38.776
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] -0.555 -0.261 0.816
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.711 r_dihedral_angle_4_deg 15.979 r_dihedral_angle_3_deg 13.623 r_dihedral_angle_1_deg 6.848 r_lrange_it 4.235 r_lrange_other 4.235 r_mcangle_it 2.718 r_mcangle_other 2.718 r_scangle_it 2.53 r_scangle_other 2.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.711 r_dihedral_angle_4_deg 15.979 r_dihedral_angle_3_deg 13.623 r_dihedral_angle_1_deg 6.848 r_lrange_it 4.235 r_lrange_other 4.235 r_mcangle_it 2.718 r_mcangle_other 2.718 r_scangle_it 2.53 r_scangle_other 2.53 r_mcbond_it 1.654 r_mcbond_other 1.654 r_scbond_it 1.515 r_scbond_other 1.515 r_angle_refined_deg 1.234 r_angle_other_deg 1.078 r_nbd_refined 0.18 r_symmetry_nbd_other 0.171 r_nbtor_refined 0.156 r_nbd_other 0.149 r_xyhbond_nbd_refined 0.139 r_symmetry_nbd_refined 0.118 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.045 r_symmetry_xyhbond_nbd_other 0.019 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_symmetry_xyhbond_nbd_refined 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9197 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 155
Software Software Software Name Purpose REFMAC refinement autoPROC data processing STARANISO data scaling PHASER phasing autoPROC data reduction