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W-formate dehydrogenase from Desulfovibrio vulgaris - Soaking with Formate 1 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 2.24 44.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.537 α = 90 b = 122.778 β = 90 c = 148.985 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 1.946 94.93 91.96 0.9971 9.2 4.33 73334
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 1.95 2.07 0.435
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 1.946 94.93 73316 3564 83.657 0.195 0.1929 0.1979 0.2427 0.2439 38.302
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] 0.093 -0.166 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.87 r_dihedral_angle_4_deg 20.114 r_dihedral_angle_3_deg 15.847 r_dihedral_angle_1_deg 7.601 r_lrange_it 6.551 r_lrange_other 6.551 r_scangle_it 5.158 r_scangle_other 5.158 r_mcangle_it 4.392 r_mcangle_other 4.392
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.87 r_dihedral_angle_4_deg 20.114 r_dihedral_angle_3_deg 15.847 r_dihedral_angle_1_deg 7.601 r_lrange_it 6.551 r_lrange_other 6.551 r_scangle_it 5.158 r_scangle_other 5.158 r_mcangle_it 4.392 r_mcangle_other 4.392 r_scbond_it 3.535 r_scbond_other 3.535 r_mcbond_it 3.229 r_mcbond_other 3.229 r_angle_refined_deg 1.618 r_angle_other_deg 1.278 r_nbd_other 0.22 r_nbd_refined 0.202 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.165 r_symmetry_nbd_refined 0.159 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.047 r_symmetry_xyhbond_nbd_refined 0.034 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9197 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 164
Software Software Software Name Purpose REFMAC refinement autoPROC data processing STARANISO data scaling PHASER phasing autoPROC data reduction