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Crystal structure of the F337A mutation 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 7S2H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.05 M Succinic Acid, 15% PEG3350, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.38 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.307 α = 90 b = 78.654 β = 100.755 c = 77.079 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 DECTRIS EIGER X 16M 2022-11-21 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) 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 40 96.1 0.081 0.045 0.982 20.1 3 30375 -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 2.4 2.44 85.7 0.43 0.25 0.838 1.9 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.4 39.582 29925 1484 96.33 0.204 0.2023 0.2446 0.2343 48.306
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] 1.136 -0.556 -3.696 2.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.333 r_dihedral_angle_3_deg 14.115 r_dihedral_angle_2_deg 10.628 r_lrange_it 6.363 r_lrange_other 6.36 r_dihedral_angle_1_deg 6.217 r_scangle_it 4.278 r_scangle_other 4.277 r_mcangle_it 3.629 r_mcangle_other 3.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.333 r_dihedral_angle_3_deg 14.115 r_dihedral_angle_2_deg 10.628 r_lrange_it 6.363 r_lrange_other 6.36 r_dihedral_angle_1_deg 6.217 r_scangle_it 4.278 r_scangle_other 4.277 r_mcangle_it 3.629 r_mcangle_other 3.628 r_scbond_it 2.761 r_scbond_other 2.76 r_mcbond_it 2.36 r_mcbond_other 2.36 r_angle_refined_deg 1.286 r_angle_other_deg 0.429 r_symmetry_xyhbond_nbd_refined 0.276 r_symmetry_nbd_refined 0.219 r_nbd_refined 0.212 r_symmetry_nbd_other 0.21 r_nbd_other 0.199 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.151 r_ncsr_local_group_1 0.12 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.057 r_symmetry_xyhbond_nbd_other 0.029 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5654 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing SERGUI data collection