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Crystal structure of Mycobacterium tuberculosis hypoxanthine guanine phosphoribosyltransferase in complex with [3S,4R]-(4-(Hypoxanthin-9-yl)pyrrolidin-3-yl)-oxymethanephosphonic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RHT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 The well solution: 20% PEG8000, 0.1 M Tris-HCl pH 8.5 and 0.2 M MgCl2. The drop consisted of an equal volume of well solution and protein inhibitor complex
Crystal Properties Matthews coefficient Solvent content 1.99 38.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.264 α = 90 b = 85.678 β = 90 c = 154.586 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 ADSC QUANTUM 270 2013-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9791 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 2.45 46.44 97.7 0.119 8 5.6 27104
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4RHT 2.45 46.44 1.35 27051 1997 96.95 0.235 0.23 0.2979 0.2581 45.4514
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 13.08 f_angle_d 0.558 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 5510 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 164
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling PHASER phasing