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Crystal structure of adenine phosphoribosyl transferase from Trypanosoma brucei in complex with AMP, pyrophosphate, and ribose-5-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QB7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 MCSG1 H10 (289135h10): 25% PEG3350, 100mM HEPES:NaOH, pH 7.5, 5mM AMP, 5mM pyrophosphate, protein conc. 23.85mg/mL, cryo 25% ethylene glycol: unique puck ID: xhs1-4
Crystal Properties Matthews coefficient Solvent content 2.1 41.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.84 α = 90 b = 72.85 β = 90 c = 85.61 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 RAYONIX MX-300 2017-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.35 50 99.7 0.04 0.045 0.999 20.54 4.877 100141 -3 13.47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.39 100 0.551 0.62 0.848 2.52 4.821
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 1qb7 1.35 50 1.34 100130 2090 99.67 0.144 0.1434 0.1438 0.175 0.1766 21.1722
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 19.103 f_angle_d 1.018 f_chiral_restr 0.09 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3629 Nucleic Acid Atoms Solvent Atoms 656 Heterogen Atoms 57
Software Software Software Name Purpose XSCALE data scaling Coot model building PHENIX refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing