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human Pyridoxine-5'-phosphate oxidase in complex with PLP-carbidopa 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 6.4 298 PEG 3350 10%, 0.1 M MES pH=6.4
Crystal Properties Matthews coefficient Solvent content 1.97 37.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.475 α = 90 b = 82.475 β = 90 c = 58.919 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 2025-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.87313 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 2.04 71.43 99.5 0.064 0.998 17.9 5.5 83270
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 2.04 2.09 0.448 0.904
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 2.04 71.425 14987 734 99.429 0.183 0.1808 0.1902 0.2265 0.2297 RANDOM 28.821
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] -0.586 -0.293 -0.586 1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.24 r_dihedral_angle_3_deg 13.551 r_dihedral_angle_2_deg 12.58 r_dihedral_angle_1_deg 6.435 r_lrange_it 5.641 r_lrange_other 5.563 r_scangle_it 3.839 r_scangle_other 3.838 r_mcangle_it 2.673 r_mcangle_other 2.673
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.24 r_dihedral_angle_3_deg 13.551 r_dihedral_angle_2_deg 12.58 r_dihedral_angle_1_deg 6.435 r_lrange_it 5.641 r_lrange_other 5.563 r_scangle_it 3.839 r_scangle_other 3.838 r_mcangle_it 2.673 r_mcangle_other 2.673 r_scbond_it 2.307 r_scbond_other 2.306 r_mcbond_it 1.739 r_mcbond_other 1.739 r_angle_refined_deg 1.432 r_angle_other_deg 0.542 r_symmetry_xyhbond_nbd_other 0.444 r_symmetry_nbd_other 0.209 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.185 r_nbd_other 0.18 r_symmetry_nbd_refined 0.112 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.072 r_bond_refined_d 0.048 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1705 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement MOLREP phasing REFMAC phasing Coot model building Aimless data scaling