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Crystal structure of H. pylori purine nucleoside phosphorylase from clinical isolate HpPNP-3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MX4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 291 0.2M NaCl, 0.1M Na/K phosphate pH 6.2, 50% PEG 200
Crystal Properties Matthews coefficient Solvent content 4.78 74.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.596 α = 90 b = 143.596 β = 90 c = 143.596 γ = 90
Symmetry Space Group P 41 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD OXFORD RUBY CCD 2015-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.541
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.4 29.311 99.4 15.2 14 20243
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5MX4 2.4 29.311 1.33 20237 1002 99.36 0.2158 0.2135 0.2148 0.2591 0.2597 37.169
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.352 f_angle_d 1.063 f_chiral_restr 0.056 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1802 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 113
Software Software Software Name Purpose PHENIX refinement SCALA data scaling PDB_EXTRACT data extraction CrysalisPro data reduction PHASER phasing