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W-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) - aerobic soaked with 100 bar Kr
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SDR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 22% PEG 3350, 0.1M Tris-HCl pH 8.0, 1M LiCl
Crystal Properties Matthews coefficient Solvent content 2.26 45.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.665 α = 90 b = 128.313 β = 90 c = 148.735 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 2022-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8610 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 1.64 97.155 96.49 0.9987 14.08 13.31 135242
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 1.64 1.733 0.6367
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 1.64 97.155 135242 6672 89.068 0.189 0.1877 0.1954 0.2187 0.2242 29.348
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] 0.216 -0.166 -0.051
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.097 r_dihedral_angle_4_deg 19.657 r_dihedral_angle_3_deg 13.044 r_dihedral_angle_1_deg 7.177 r_lrange_it 5.362 r_lrange_other 5.325 r_scangle_it 4.267 r_scangle_other 4.267 r_mcangle_it 3.238 r_mcangle_other 3.238
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.097 r_dihedral_angle_4_deg 19.657 r_dihedral_angle_3_deg 13.044 r_dihedral_angle_1_deg 7.177 r_lrange_it 5.362 r_lrange_other 5.325 r_scangle_it 4.267 r_scangle_other 4.267 r_mcangle_it 3.238 r_mcangle_other 3.238 r_scbond_it 2.942 r_scbond_other 2.941 r_mcbond_it 2.454 r_mcbond_other 2.454 r_angle_refined_deg 1.648 r_angle_other_deg 1.37 r_nbd_refined 0.213 r_nbd_other 0.189 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.085 r_symmetry_xyhbond_nbd_refined 0.085 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.063 r_symmetry_nbd_refined 0.057 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 593 Heterogen Atoms 187
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