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Oxidoreductase from Phytophthora sojae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Z5Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, 30% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.57 52.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.267 α = 90 b = 73.129 β = 90 c = 116.418 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 16M 2023-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.98 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.789 61.925 100 0.998 16.3 13.3 38093
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 1.789 1.82 0.829
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.789 61.925 38093 1905 99.974 0.163 0.1608 0.2023 0.2072 27.585
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] 0.746 -1.326 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.198 r_dihedral_angle_3_deg 15.028 r_lrange_it 8.645 r_lrange_other 8.637 r_dihedral_angle_1_deg 7.218 r_scangle_it 7.111 r_scangle_other 7.072 r_dihedral_angle_2_deg 4.984 r_scbond_it 4.634 r_scbond_other 4.591
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.198 r_dihedral_angle_3_deg 15.028 r_lrange_it 8.645 r_lrange_other 8.637 r_dihedral_angle_1_deg 7.218 r_scangle_it 7.111 r_scangle_other 7.072 r_dihedral_angle_2_deg 4.984 r_scbond_it 4.634 r_scbond_other 4.591 r_mcangle_it 4.144 r_mcangle_other 4.144 r_mcbond_it 2.893 r_mcbond_other 2.893 r_angle_refined_deg 1.56 r_angle_other_deg 0.558 r_nbd_refined 0.218 r_symmetry_nbd_other 0.204 r_xyhbond_nbd_refined 0.203 r_nbtor_refined 0.185 r_nbd_other 0.149 r_symmetry_xyhbond_nbd_refined 0.117 r_symmetry_nbd_refined 0.102 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.086 r_metal_ion_refined 0.055 r_symmetry_xyhbond_nbd_other 0.031 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2686 Nucleic Acid Atoms Solvent Atoms 366 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement AutoProcess data reduction Aimless data scaling MOLREP phasing