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W-formate dehydrogenase from Desulfovibrio vulgaris - Soaking with Formate 1.5 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 38.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.361 α = 90 b = 127.456 β = 90 c = 128.952 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 1.61 90.65 94.14 0.996 9.5 5.7 94816
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 1.61 1.78 0.6555
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 1.61 90.65 94816 4778 68.517 0.152 0.1509 0.1629 0.1754 0.1851 19.364
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] 0.132 -0.062 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.373 r_dihedral_angle_4_deg 19.159 r_dihedral_angle_3_deg 13.409 r_lrange_it 7.282 r_lrange_other 7.264 r_dihedral_angle_1_deg 6.894 r_scangle_it 6.18 r_scangle_other 6.18 r_scbond_other 4.572 r_scbond_it 4.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.373 r_dihedral_angle_4_deg 19.159 r_dihedral_angle_3_deg 13.409 r_lrange_it 7.282 r_lrange_other 7.264 r_dihedral_angle_1_deg 6.894 r_scangle_it 6.18 r_scangle_other 6.18 r_scbond_other 4.572 r_scbond_it 4.56 r_mcangle_it 3.913 r_mcangle_other 3.913 r_mcbond_other 2.927 r_mcbond_it 2.926 r_angle_refined_deg 1.601 r_angle_other_deg 1.452 r_symmetry_xyhbond_nbd_refined 0.286 r_nbd_other 0.213 r_nbd_refined 0.211 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.146 r_symmetry_nbd_refined 0.142 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9126 Nucleic Acid Atoms Solvent Atoms 557 Heterogen Atoms 230
Software Software Software Name Purpose REFMAC refinement autoPROC data processing STARANISO data scaling PHASER phasing autoPROC data reduction