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Crystal structure of full-length of APS kinase from Entamoeba histolytica
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 10 mM Tris-HCl (pH 8.0)
100 mM NaCl
1 mM TCEP
5 mM APS
5 mM AMP-PNP
5 mM MgCl2
0.24 M K2SO4
16% PEG3400
Crystal Properties Matthews coefficient Solvent content 2.91 57.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.449 α = 90 b = 158.387 β = 90 c = 226.163 γ = 90
Symmetry Space Group C 2 2 21
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 2023-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.59 50 99.5 0.066 0.999 14.36 6.1 79795
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 2.59 2.75 0.531 0.8
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 2.595 19.97 79596 3995 99.308 0.228 0.2265 0.2302 0.2648 0.2658 111.398
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] -0.001 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.224 r_lrange_other 15.981 r_lrange_it 15.98 r_dihedral_angle_6_deg 13.515 r_scangle_it 11.812 r_scangle_other 11.798 r_dihedral_angle_2_deg 11.572 r_mcangle_it 11.337 r_mcangle_other 11.336 r_scbond_it 7.562
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.224 r_lrange_other 15.981 r_lrange_it 15.98 r_dihedral_angle_6_deg 13.515 r_scangle_it 11.812 r_scangle_other 11.798 r_dihedral_angle_2_deg 11.572 r_mcangle_it 11.337 r_mcangle_other 11.336 r_scbond_it 7.562 r_scbond_other 7.55 r_mcbond_it 7.388 r_mcbond_other 7.387 r_dihedral_angle_1_deg 5.899 r_angle_refined_deg 1.285 r_angle_other_deg 0.769 r_nbd_other 0.237 r_nbd_refined 0.221 r_symmetry_nbd_other 0.214 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.137 r_symmetry_xyhbond_nbd_refined 0.118 r_symmetry_nbd_refined 0.114 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.07 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14065 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling CRANK2 phasing BUCCANEER model building