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W-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystallized with Formate and Reoxidized by exposure to air for 12 min
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SDV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 26% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl, 10 mM sodium formate
Crystal Properties Matthews coefficient Solvent content 2.32 47.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.8 α = 90 b = 127.594 β = 90 c = 148.622 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 PILATUS 6M 2022-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9686 ESRF ID30B
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 1.906 96.999 94.46 0.9967 9.086 10.95 82382
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 1.906 2.008 0.62
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 6SDV 1.906 96.999 82370 4045 85.037 0.19 0.1878 0.196 0.2251 0.233 33.79
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] 0.147 -0.173 0.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.14 r_dihedral_angle_4_deg 17.859 r_dihedral_angle_3_deg 13.431 r_dihedral_angle_1_deg 7.022 r_lrange_other 6.624 r_lrange_it 6.617 r_scangle_it 5.259 r_scangle_other 5.258 r_mcangle_it 4.585 r_mcangle_other 4.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.14 r_dihedral_angle_4_deg 17.859 r_dihedral_angle_3_deg 13.431 r_dihedral_angle_1_deg 7.022 r_lrange_other 6.624 r_lrange_it 6.617 r_scangle_it 5.259 r_scangle_other 5.258 r_mcangle_it 4.585 r_mcangle_other 4.585 r_scbond_it 3.592 r_scbond_other 3.592 r_mcbond_it 3.32 r_mcbond_other 3.32 r_angle_refined_deg 1.278 r_angle_other_deg 1.154 r_nbd_refined 0.189 r_symmetry_nbd_other 0.176 r_nbd_other 0.172 r_nbtor_refined 0.159 r_xyhbond_nbd_refined 0.134 r_symmetry_xyhbond_nbd_refined 0.127 r_symmetry_nbd_refined 0.115 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.056 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9234 Nucleic Acid Atoms Solvent Atoms 373 Heterogen Atoms 162
Software Software Software Name Purpose REFMAC refinement autoPROC data processing STARANISO data scaling PHASER phasing autoPROC data reduction