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Oxidoreductase B from Phytophthora sojae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 0.1M sodium acetate trihydrate pH 4.5, 2.0M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.11 41.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.067 α = 90 b = 106.897 β = 114.099 c = 44.815 γ = 90
Symmetry Space Group P 1 21 1
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 4M 2023-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.97 ESRF MASSIF-3
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 1.9 53.42 99.4 0.989 6.6 7.3 26881
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 2.05 2.09 0.768
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 2.05 53.42 21448 1027 99.204 0.171 0.168 0.177 0.2322 0.2328 26.66
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] 0.595 -0.096 -1.553 0.745
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.988 r_dihedral_angle_6_deg 15.725 r_lrange_it 7.196 r_dihedral_angle_1_deg 7.155 r_lrange_other 7.153 r_dihedral_angle_2_deg 6.319 r_scangle_it 5.4 r_scangle_other 5.399 r_mcangle_other 3.45 r_mcangle_it 3.449
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.988 r_dihedral_angle_6_deg 15.725 r_lrange_it 7.196 r_dihedral_angle_1_deg 7.155 r_lrange_other 7.153 r_dihedral_angle_2_deg 6.319 r_scangle_it 5.4 r_scangle_other 5.399 r_mcangle_other 3.45 r_mcangle_it 3.449 r_scbond_it 3.431 r_scbond_other 3.431 r_mcbond_it 2.395 r_mcbond_other 2.378 r_angle_refined_deg 1.436 r_angle_other_deg 0.474 r_symmetry_nbd_refined 0.231 r_symmetry_xyhbond_nbd_refined 0.223 r_nbd_other 0.222 r_symmetry_nbd_other 0.205 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.183 r_symmetry_nbtor_other 0.085 r_metal_ion_refined 0.077 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_symmetry_xyhbond_nbd_other 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2710 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement xia2 data reduction TRUNCATE data scaling MOLREP phasing