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Entamoeba histolytica Pyruvate kinase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 289 50mM MES buffer, pH 6.2, 0.2M LiCl2, 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 1.93 36.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.801 α = 90 b = 89.536 β = 90 c = 37.138 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 6M 2021-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.977 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.75 42.937 99 0.115 0.109 0.047 0.998 15.5 9.3 29332
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 1.75 1.78 99.1 0.956 0.485 0.718 2 9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 1.75 42.937 29295 1526 98.7 0.172 0.1706 0.1779 0.2017 0.208 22.543
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] -1.628 -1.505 3.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.425 r_dihedral_angle_3_deg 13.606 r_dihedral_angle_2_deg 10.242 r_lrange_it 7.242 r_lrange_other 7.227 r_dihedral_angle_1_deg 6.814 r_scangle_it 6.376 r_scangle_other 6.374 r_scbond_other 4.359 r_scbond_it 4.358
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.425 r_dihedral_angle_3_deg 13.606 r_dihedral_angle_2_deg 10.242 r_lrange_it 7.242 r_lrange_other 7.227 r_dihedral_angle_1_deg 6.814 r_scangle_it 6.376 r_scangle_other 6.374 r_scbond_other 4.359 r_scbond_it 4.358 r_mcangle_other 3.145 r_mcangle_it 3.143 r_mcbond_it 2.4 r_mcbond_other 2.396 r_angle_refined_deg 1.899 r_angle_other_deg 0.617 r_xyhbond_nbd_refined 0.264 r_symmetry_xyhbond_nbd_refined 0.229 r_nbd_refined 0.226 r_symmetry_nbd_refined 0.205 r_symmetry_nbd_other 0.2 r_nbd_other 0.188 r_nbtor_refined 0.179 r_xyhbond_nbd_other 0.13 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_symmetry_xyhbond_nbd_other 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2551 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling SHELXCD phasing