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A divergent kinase lacking the glycine-rich loop regulates membrane ultrastructure of the Toxoplasma parasitophorous vacuole
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.4 298 0.2M Proline, 0.1M HEPES 7.4, 10% PEG-3350
Crystal Properties Matthews coefficient Solvent content 2.12 41.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.466 α = 90 b = 123.068 β = 90 c = 86.615 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 100 CCD ADSC QUANTUM 315r 2015-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.038 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.5 50 99.9 0.088 0.095 0.034 9.5 8 64181
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 99.8 0.855 0.925 0.345 0.761 7.3
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 SAD THROUGHOUT 2.5 47.7 58472 2987 90.9 0.1993 0.19721 0.1998 0.23877 0.2402 RANDOM 43.39
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] 0.94 -0.47 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.512 r_dihedral_angle_4_deg 20.996 r_dihedral_angle_3_deg 14.362 r_long_range_B_other 10.311 r_long_range_B_refined 10.305 r_scangle_other 7.707 r_dihedral_angle_1_deg 6.374 r_mcangle_it 6.15 r_mcangle_other 6.15 r_scbond_it 5.359
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.512 r_dihedral_angle_4_deg 20.996 r_dihedral_angle_3_deg 14.362 r_long_range_B_other 10.311 r_long_range_B_refined 10.305 r_scangle_other 7.707 r_dihedral_angle_1_deg 6.374 r_mcangle_it 6.15 r_mcangle_other 6.15 r_scbond_it 5.359 r_scbond_other 5.358 r_mcbond_it 4.079 r_mcbond_other 4.079 r_angle_refined_deg 1.244 r_angle_other_deg 0.852 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 12413 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SHELXDE phasing PDB_EXTRACT data extraction