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W-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystallized with Formate and Reoxidized by exposure to air for 1 h in the absence 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 22% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.26 45.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.558 α = 90 b = 128.006 β = 90 c = 148.905 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 2021-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.7749 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 1.664 97.258 90.6 0.9956 7.992 4.66 108396
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 1.664 1.792 0.6281
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 1.664 97.258 108396 5448 74.709 0.196 0.1939 0.2034 0.2322 0.2401 30.649
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] 0.321 -0.25 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.365 r_dihedral_angle_4_deg 19.753 r_dihedral_angle_3_deg 14.003 r_dihedral_angle_1_deg 7.342 r_lrange_it 5.009 r_lrange_other 4.975 r_scangle_it 3.754 r_scangle_other 3.754 r_mcangle_it 3.196 r_mcangle_other 3.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.365 r_dihedral_angle_4_deg 19.753 r_dihedral_angle_3_deg 14.003 r_dihedral_angle_1_deg 7.342 r_lrange_it 5.009 r_lrange_other 4.975 r_scangle_it 3.754 r_scangle_other 3.754 r_mcangle_it 3.196 r_mcangle_other 3.196 r_scbond_it 2.452 r_scbond_other 2.452 r_mcbond_it 2.235 r_mcbond_other 2.235 r_angle_refined_deg 1.511 r_angle_other_deg 1.269 r_nbd_refined 0.204 r_symmetry_nbd_other 0.185 r_nbd_other 0.184 r_nbtor_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.162 r_xyhbond_nbd_refined 0.154 r_symmetry_nbd_refined 0.096 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.077 r_symmetry_xyhbond_nbd_other 0.052 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 569 Heterogen Atoms 168
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