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W-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystallized with Formate and Reoxidized by exposure to air (in a not degassed drop) for 34 min in the presence of Formate
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 24% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.22 44.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.433 α = 90 b = 123.085 β = 90 c = 148.138 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 PILATUS3 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 2.11 94.67 91.15 0.996 8.4 8.9 54097
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 2.11 2.28 0.591
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 2.11 94.67 54095 2723 78.843 0.201 0.1991 0.209 0.2404 0.2469 38.678
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] 0.269 -0.3 0.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.644 r_dihedral_angle_4_deg 15.849 r_dihedral_angle_3_deg 13.162 r_lrange_it 8.759 r_lrange_other 8.758 r_scangle_it 7.166 r_scangle_other 7.166 r_dihedral_angle_1_deg 6.725 r_mcangle_it 6.409 r_mcangle_other 6.409
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.644 r_dihedral_angle_4_deg 15.849 r_dihedral_angle_3_deg 13.162 r_lrange_it 8.759 r_lrange_other 8.758 r_scangle_it 7.166 r_scangle_other 7.166 r_dihedral_angle_1_deg 6.725 r_mcangle_it 6.409 r_mcangle_other 6.409 r_scbond_it 5.062 r_scbond_other 5.062 r_mcbond_other 4.789 r_mcbond_it 4.788 r_angle_refined_deg 1.212 r_angle_other_deg 1.072 r_nbd_refined 0.176 r_symmetry_nbd_other 0.169 r_nbd_other 0.163 r_symmetry_nbd_refined 0.162 r_nbtor_refined 0.155 r_xyhbond_nbd_refined 0.125 r_symmetry_xyhbond_nbd_refined 0.086 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.045 r_symmetry_xyhbond_nbd_other 0.011 r_bond_refined_d 0.003 r_gen_planes_refined 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 9159 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 157
Software Software Software Name Purpose REFMAC refinement autoPROC data processing STARANISO data scaling PHASER phasing XDS data reduction Aimless data scaling XSCALE data scaling pointless data scaling