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W-formate dehydrogenase from Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) - aerobic soaked with 55 bar oxygen
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 2.27 45.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.837 α = 90 b = 128.376 β = 90 c = 148.809 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 2022-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8731 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 1.83 45.68 99.8 0.992 5.8 5.5 109987
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 1.83 1.86 0.204
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 1.83 43.651 109896 5550 99.742 0.197 0.1945 0.2034 0.2412 0.2467 29.742
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] -0.345 -0.952 1.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.105 r_dihedral_angle_4_deg 19.126 r_dihedral_angle_3_deg 13.939 r_dihedral_angle_1_deg 7.382 r_lrange_it 4.76 r_lrange_other 4.75 r_scangle_it 3.564 r_scangle_other 3.563 r_mcangle_it 2.866 r_mcangle_other 2.866
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.105 r_dihedral_angle_4_deg 19.126 r_dihedral_angle_3_deg 13.939 r_dihedral_angle_1_deg 7.382 r_lrange_it 4.76 r_lrange_other 4.75 r_scangle_it 3.564 r_scangle_other 3.563 r_mcangle_it 2.866 r_mcangle_other 2.866 r_scbond_it 2.307 r_scbond_other 2.306 r_mcbond_it 1.956 r_mcbond_other 1.954 r_angle_refined_deg 1.495 r_angle_other_deg 1.255 r_nbd_refined 0.202 r_nbd_other 0.183 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.165 r_symmetry_nbd_refined 0.157 r_xyhbond_nbd_refined 0.125 r_symmetry_xyhbond_nbd_refined 0.105 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9234 Nucleic Acid Atoms Solvent Atoms 403 Heterogen Atoms 184
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