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Crystal structure of Trypanosoma brucei hypoxanthine-guanine phosphoribosyltranferase in complex with XMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JSQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 25% PEG 3350, 0.2 M lithium sulfate and 0.1 M Bis-Tris
Crystal Properties Matthews coefficient Solvent content 2.39 48.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.57 α = 90 b = 94.37 β = 111.97 c = 45 γ = 90
Symmetry Space Group C 1 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 2016-02-02 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) 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 2.39 71.35 99.6 0.125 0.06 10 5.2 17999
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.39 2.52 97.4 0.8 0.397 2.1 5
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 5JSQ 2.392 47.185 1.34 16212 1787 99.63 0.2613 0.2571 0.256 0.285 0.2832
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 13.394 f_angle_d 0.621 f_chiral_restr 0.024 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2666 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction SCALA data scaling PHASER phasing