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Human Pyridoxine-5'-phosphate oxidase in complex with PLP-isoniazid 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 6.4 294 MES 0.1 M pH=6.4; PEG 3350 12%
Crystal Properties Matthews coefficient Solvent content 1.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.707 α = 90 b = 82.707 β = 90 c = 59.191 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 2026-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 1 ESRF ID30B
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 2.2 45.7 91.7 0.066 0.998 9.3 3.4 11043
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 2.2 2.27 81 0.932 0.94 3.4
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 2.2 45.669 11036 553 90.637 0.176 0.1731 0.1801 0.2354 0.238 50.023
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] -0.18 -0.09 -0.18 0.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.552 r_dihedral_angle_3_deg 12.164 r_lrange_it 8.933 r_lrange_other 8.932 r_dihedral_angle_1_deg 6.944 r_scangle_it 6.916 r_scangle_other 6.914 r_dihedral_angle_2_deg 5.653 r_mcangle_other 4.953 r_mcangle_it 4.945
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.552 r_dihedral_angle_3_deg 12.164 r_lrange_it 8.933 r_lrange_other 8.932 r_dihedral_angle_1_deg 6.944 r_scangle_it 6.916 r_scangle_other 6.914 r_dihedral_angle_2_deg 5.653 r_mcangle_other 4.953 r_mcangle_it 4.945 r_scbond_it 4.356 r_scbond_other 4.354 r_mcbond_it 3.523 r_mcbond_other 3.514 r_angle_refined_deg 1.356 r_angle_other_deg 0.478 r_symmetry_nbd_other 0.203 r_nbd_refined 0.189 r_nbtor_refined 0.187 r_nbd_other 0.164 r_xyhbond_nbd_refined 0.153 r_symmetry_xyhbond_nbd_refined 0.145 r_symmetry_nbd_refined 0.129 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.063 r_symmetry_xyhbond_nbd_other 0.05 r_gen_planes_refined 0.008 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1705 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement MOLREP phasing autoPROC data processing Aimless data scaling