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Crystal structure of Trypanosoma cruzi glucokinase in complex with inhibitor BENZ-GlcN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q2R PDB entry 2Q2R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 A glucose-free TcGlcK crystal was soaked in 1.0 mM BENZ-GlcN, 5.0% (v/v) DMSO, 0.1 M sodium citrate (pH 7.0), 20% (w/v) PEG 3,350 for 28 hours
Crystal Properties Matthews coefficient Solvent content 2.54 51.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.567 α = 90 b = 78.837 β = 94.5 c = 76.605 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 PIXEL ADSC HF-4M ADSC HF-4M PIXEL ARRAY DETECTOR 2015-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97910 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 2.4 76.37 98.5 0.079 0.041 0.998 12.9 4.3 31494 51.07
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 92 0.822 0.454 0.592 1.4 3.7 3076
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 THROUGHOUT PDB entry 2Q2R 2.4 49.056 1.93 28819 1526 95.57 0.1961 0.1929 0.1968 0.2564 0.2563 42.51
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 15.763 f_angle_d 1.172 f_chiral_restr 0.074 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5696 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 40
Software Software Software Name Purpose Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction