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W-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) - anaerobic soaked with 50 bar CO2 for 1 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 298 22% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.3 46.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.027 α = 90 b = 128.724 β = 90 c = 149.861 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 EIGER X 9M 2022-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9184 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 2.069 59.653 93.92 0.9932 7.604 5.96 57216
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 2.069 2.277 0.526
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.069 59.653 57215 2831 73.731 0.213 0.211 0.2184 0.2549 0.2621 41.914
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] 0.242 -0.255 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.895 r_dihedral_angle_4_deg 16.206 r_dihedral_angle_3_deg 12.935 r_dihedral_angle_1_deg 6.672 r_lrange_it 6.665 r_lrange_other 6.664 r_mcangle_it 4.906 r_mcangle_other 4.905 r_scangle_it 4.621 r_scangle_other 4.613
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.895 r_dihedral_angle_4_deg 16.206 r_dihedral_angle_3_deg 12.935 r_dihedral_angle_1_deg 6.672 r_lrange_it 6.665 r_lrange_other 6.664 r_mcangle_it 4.906 r_mcangle_other 4.905 r_scangle_it 4.621 r_scangle_other 4.613 r_mcbond_it 3.236 r_mcbond_other 3.236 r_scbond_it 3.057 r_scbond_other 3.029 r_angle_refined_deg 1.229 r_angle_other_deg 1.08 r_nbd_refined 0.179 r_symmetry_xyhbond_nbd_refined 0.172 r_symmetry_nbd_other 0.169 r_nbtor_refined 0.155 r_nbd_other 0.149 r_xyhbond_nbd_refined 0.134 r_symmetry_nbd_refined 0.082 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.046 r_symmetry_xyhbond_nbd_other 0.035 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 9243 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 206
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