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human pyridoxine 5-phosphate oxidase in complex with Z isomer of pyridoxilidenrhodanine 5-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NRG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 12% PEG 6000, 0.1 lithium sulfate, 0.1 sodium citrate
Crystal Properties Matthews coefficient Solvent content 1.97 37.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.15 α = 90 b = 83.15 β = 90 c = 59.17 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 PILATUS 6M 2021-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
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 1.553 45.758 100 1 24.9 18.3 34420
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 1.553 1.58 0.803
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 THROUGHOUT 1.553 45.758 34420 1675 99.962 0.165 0.1627 0.2004 0.2102 27.431
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] -0.499 -0.25 -0.499 1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.651 r_dihedral_angle_other_3_deg 24.047 r_dihedral_angle_4_deg 17.921 r_dihedral_angle_3_deg 12.877 r_lrange_it 6.831 r_lrange_other 6.787 r_dihedral_angle_1_deg 6.689 r_scangle_it 5.551 r_scangle_other 5.549 r_scbond_it 3.756
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.651 r_dihedral_angle_other_3_deg 24.047 r_dihedral_angle_4_deg 17.921 r_dihedral_angle_3_deg 12.877 r_lrange_it 6.831 r_lrange_other 6.787 r_dihedral_angle_1_deg 6.689 r_scangle_it 5.551 r_scangle_other 5.549 r_scbond_it 3.756 r_scbond_other 3.754 r_mcangle_it 3.066 r_mcangle_other 3.066 r_mcbond_it 2.232 r_mcbond_other 2.227 r_angle_refined_deg 1.768 r_angle_other_deg 1.435 r_xyhbond_nbd_refined 0.219 r_nbd_refined 0.2 r_symmetry_nbd_refined 0.196 r_symmetry_nbd_other 0.19 r_nbd_other 0.186 r_nbtor_refined 0.179 r_symmetry_xyhbond_nbd_refined 0.147 r_chiral_restr 0.098 r_symmetry_xyhbond_nbd_other 0.086 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 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 192 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling MOLREP phasing