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Crystal structure of E. coli hypoxanthine phosphoribosyltransferase in complexed with 9-[N,N-(Bis-3-phosphonopropyl)aminomethyl]-9-deazahypoxanthine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G9S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.1 M HEPES pH 7.5 and 0.1 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 4.23 70.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.975 α = 90 b = 84.975 β = 90 c = 167.723 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 CCD ADSC QUANTUM 270 2013-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
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 2.808 44.52 99.5 0.119 0.997 10.8 17700
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 1G9S 2.808 44.518 1.34 17655 1746 99.5 0.1804 0.1758 0.1888 0.2213 0.2231 42.1829
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 12.256 f_angle_d 0.636 f_chiral_restr 0.022 f_bond_d 0.005 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2706 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 69
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing