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W-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystallized with Formate and Exposed to air for 0 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 22% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.22 44.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.988 α = 90 b = 124.345 β = 90 c = 149.899 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 2022-07-03 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 47.898 99.6 0.994 6.6 7 82099
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 2.04 0.527
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 2.005 47.898 82000 4152 99.706 0.183 0.1811 0.1881 0.2195 0.226 31.242
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] 0.796 -1.28 0.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.145 r_dihedral_angle_3_deg 12.971 r_dihedral_angle_1_deg 6.724 r_lrange_it 6.5 r_lrange_other 6.424 r_dihedral_angle_2_deg 5.388 r_scangle_it 4.774 r_scangle_other 4.773 r_mcangle_it 3.969 r_mcangle_other 3.968
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.145 r_dihedral_angle_3_deg 12.971 r_dihedral_angle_1_deg 6.724 r_lrange_it 6.5 r_lrange_other 6.424 r_dihedral_angle_2_deg 5.388 r_scangle_it 4.774 r_scangle_other 4.773 r_mcangle_it 3.969 r_mcangle_other 3.968 r_scbond_it 3.286 r_scbond_other 3.286 r_mcbond_it 2.873 r_mcbond_other 2.872 r_angle_refined_deg 1.052 r_angle_other_deg 0.362 r_symmetry_nbd_refined 0.243 r_nbd_other 0.208 r_nbd_refined 0.2 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.151 r_xyhbond_nbd_refined 0.124 r_metal_ion_refined 0.081 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.058 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 9211 Nucleic Acid Atoms Solvent Atoms 422 Heterogen Atoms 171
Software Software Software Name Purpose REFMAC refinement autoPROC data processing Aimless data scaling PHASER phasing XDS data reduction Aimless data scaling XSCALE data scaling pointless data scaling