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Crystal structure of H. pylori purine nucleoside phosphorylase in complex with PO4 and formycin A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 0.1M TRIS-HCl, 10% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.24 44.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.893 α = 90 b = 85.895 β = 90 c = 269.306 γ = 90
Symmetry Space Group P 21 21 21
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 2M 2016-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.694 48.331 98.8 0.072 0.084 0.042 12.1 3.8 153224 153224 17.26
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 95.6 0.538 0.538 0.635 0.331 1.4 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FREE R-VALUE 1.694 42.947 1.97 153104 7640 98.69 0.1986 0.1963 0.2439 0.2403 21.1427
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 15.717 f_angle_d 0.9 f_chiral_restr 0.054 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10741 Nucleic Acid Atoms Solvent Atoms 907 Heterogen Atoms 196
Software Software Software Name Purpose PHENIX refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing