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Crystal structure of the calcium-dependent kinase from toxoplasma gondii, 541.m00134, kinase domain.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 25% PEG3350, 0.2 M NaCl, 0.1 M Hepes, 5 % ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.54 51.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.345 α = 90 b = 121.345 β = 90 c = 45.521 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2008-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.17 85.75 99.9 0.087 0.097 10.7 7.3 17797 17780 47.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.17 2.25 99.7 0.62 0.62 2.72 7.1 1726
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.17 50 17784 17770 904 99.92 0.232 0.232 0.23 0.2241 0.265 0.2608 RANDOM 44.574
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] -0.23 -0.23 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.347 r_dihedral_angle_4_deg 15.601 r_dihedral_angle_3_deg 13.494 r_dihedral_angle_1_deg 4.371 r_angle_refined_deg 0.866 r_scangle_it 0.432 r_scbond_it 0.304 r_nbtor_refined 0.291 r_mcangle_it 0.267 r_symmetry_vdw_refined 0.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.347 r_dihedral_angle_4_deg 15.601 r_dihedral_angle_3_deg 13.494 r_dihedral_angle_1_deg 4.371 r_angle_refined_deg 0.866 r_scangle_it 0.432 r_scbond_it 0.304 r_nbtor_refined 0.291 r_mcangle_it 0.267 r_symmetry_vdw_refined 0.159 r_nbd_refined 0.157 r_mcbond_it 0.152 r_xyhbond_nbd_refined 0.096 r_chiral_restr 0.057 r_symmetry_hbond_refined 0.022 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2021 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction