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Crystal structure of Trypanosoma cruzi glycerol kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold A0A2V2W444
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 20% w/v Polyethylene glycol 3350, 200 mM Magnesium Formate
Crystal Properties Matthews coefficient Solvent content 2.32 46.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.779 α = 117.35 b = 89.321 β = 88.99 c = 97.155 γ = 93.68
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 PILATUS 2M 2022-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.07 44.61 93.84 0.997 5.6 1.9 117172
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.07 2.11 0.518
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 (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 2.07 44.61 111348 5822 93.84 0.17899 0.17598 0.1839 0.23753 0.2396 RANDOM 44.092
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] -0.26 -0.71 -0.18 -0.6 0.9 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.397 r_dihedral_angle_2_deg 17.627 r_dihedral_angle_1_deg 8.376 r_long_range_B_refined 8.017 r_long_range_B_other 8.011 r_scangle_other 6.451 r_mcangle_it 4.981 r_mcangle_other 4.981 r_scbond_it 4.725 r_scbond_other 4.725
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.397 r_dihedral_angle_2_deg 17.627 r_dihedral_angle_1_deg 8.376 r_long_range_B_refined 8.017 r_long_range_B_other 8.011 r_scangle_other 6.451 r_mcangle_it 4.981 r_mcangle_other 4.981 r_scbond_it 4.725 r_scbond_other 4.725 r_mcbond_it 3.672 r_mcbond_other 3.667 r_angle_refined_deg 2.298 r_angle_other_deg 0.776 r_chiral_restr 0.112 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15975 Nucleic Acid Atoms Solvent Atoms 403 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing