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Crystal structure of Trypanosoma cruzi glucokinase in the apo form (open conformation)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q2R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 1.0 uL of 7.4 mg/mL wt-TcGlcK in buffered solution [50 mM HEPES (pH 7.5), 0.2 M imidazole, 2 mM magnesium chloride] + 1.0 uL of precipitant solution [14% (w/v) PEG 3350, 0.1 M sodium citrate tribasic] was equilibrated against 85 uL of the precipitant solution using a 96-well sitting-drop plate (Innovadyne)
Crystal Properties Matthews coefficient Solvent content 2.37 48.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.304 α = 90 b = 78.92 β = 101.3 c = 76.847 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 RAYONIX MX300-HS 2014-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.8 40 100 0.083 0.031 41.9 7.5 72625 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 0.949 0.344 0.833 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2Q2R 1.8 35.92 68906 3676 99.27 0.1664 0.1649 0.1725 0.1937 0.1967 RANDOM 33.742
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] -3.21 0.93 2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.636 r_dihedral_angle_4_deg 15.309 r_dihedral_angle_3_deg 12.638 r_dihedral_angle_1_deg 6.316 r_angle_other_deg 2.347 r_angle_refined_deg 1.719 r_chiral_restr 0.087 r_bond_other_d 0.036 r_gen_planes_other 0.019 r_bond_refined_d 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.636 r_dihedral_angle_4_deg 15.309 r_dihedral_angle_3_deg 12.638 r_dihedral_angle_1_deg 6.316 r_angle_other_deg 2.347 r_angle_refined_deg 1.719 r_chiral_restr 0.087 r_bond_other_d 0.036 r_gen_planes_other 0.019 r_bond_refined_d 0.013 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5642 Nucleic Acid Atoms Solvent Atoms 548 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing