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Crystal structure of E. Coli purine nucleoside phosphorylase with PO4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K9S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 291 50mM citric buffer, 34% ammonium sulphate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.4 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.076 α = 90 b = 123.435 β = 90 c = 189.85 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 CCD MARMOSAIC 225 mm CCD 2010-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95373 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 47.463 98 0.103 18.64 99205 97448 2 2 24.459
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.12 96.4 0.462 4.9
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 1K9S 2 47.46 1.99 99325 97186 4873 98.11 0.155 0.152 0.15 0.1497 0.196 0.195 RANDOM 21.126
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] -4.548 -7.379 11.927
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.004 f_angle_d 1.059 f_chiral_restr 0.074 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10534 Nucleic Acid Atoms Solvent Atoms 1112 Heterogen Atoms 70
Software Software Software Name Purpose PHENIX refinement XSCALE data processing PDB_EXTRACT data extraction HKL-2000 data collection XDS data reduction XSCALE data scaling PHENIX phasing