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Crystal structure of Trypanosoma brucei hypoxanthine-guanine-xanthine phosphoribosyltranferase in complex with GMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AP2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293.15 25% PEG 3350, 0.2 M lithium sulphate and 0.1 M Bis-Tris pH 5
Crystal Properties Matthews coefficient Solvent content 2.07 40.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.021 α = 90 b = 107.321 β = 96.93 c = 117.214 γ = 90
Symmetry Space Group P 1 21 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 2017-04-06 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 1.99 44.744 99.9 0.088 0.061 11.3 5.7 102156
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.03 98.7 0.213 3 2.8
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 6AP2 1.993 44.744 1.36 102113 1999 99.9 0.1533 0.1524 0.1536 0.1997 0.2013
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 6.987 f_angle_d 1.151 f_chiral_restr 0.076 f_bond_d 0.013 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10337 Nucleic Acid Atoms Solvent Atoms 1251 Heterogen Atoms 155
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing