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human Pyridoxine-5'-phosphate oxidase in complex with PLP-phenelzine in its active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8QYT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 293 PEG 3350 12%, MES 0.1 M pH=6.4
Crystal Properties Matthews coefficient Solvent content 1.97 37.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.941 α = 90 b = 82.941 β = 90 c = 59.539 γ = 120
Symmetry Space Group P 31 2 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 EIGER2 X 9M 2025-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.89 41.505 99.8 0.089 0.999 15 10 19254
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.93 0.901 0.815 2.5 8.8
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.89 41.505 19243 973 99.844 0.188 0.1862 0.1977 0.2253 0.2394 RANDOM 29.038
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] -1.024 -0.512 -1.024 3.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 14.558 r_dihedral_angle_6_deg 13.154 r_dihedral_angle_3_deg 11.724 r_dihedral_angle_1_deg 6.667 r_dihedral_angle_2_deg 6.037 r_lrange_it 5.238 r_lrange_other 5.171 r_scangle_it 3.701 r_scangle_other 3.7 r_mcangle_it 2.564
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 14.558 r_dihedral_angle_6_deg 13.154 r_dihedral_angle_3_deg 11.724 r_dihedral_angle_1_deg 6.667 r_dihedral_angle_2_deg 6.037 r_lrange_it 5.238 r_lrange_other 5.171 r_scangle_it 3.701 r_scangle_other 3.7 r_mcangle_it 2.564 r_mcangle_other 2.563 r_scbond_it 2.219 r_scbond_other 2.218 r_mcbond_it 1.609 r_mcbond_other 1.608 r_angle_refined_deg 1.116 r_angle_other_deg 0.422 r_nbd_refined 0.188 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.131 r_nbd_other 0.115 r_symmetry_xyhbond_nbd_refined 0.11 r_symmetry_nbd_refined 0.107 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.057 r_gen_planes_refined 0.005 r_bond_refined_d 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 1714 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement MOLREP phasing Aimless data scaling REFMAC refinement Coot model building