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Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with bumped kinase inhibitor NA-PP2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I79
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 sitting drop vapor diffusion 6.5 298 26% PEG 3350, 0.25 M ammonium citrate, 4 mM NA-PP2; directly frozen from mother liquor, pH 6.5, sitting drop vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.03 39.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.139 α = 90 b = 72.522 β = 103.76 c = 67.116 γ = 90
Symmetry Space Group P 1 21 1
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 MARMOSAIC 325 mm CCD 2009-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97911 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.98 50 98.1 0.09 9.2 3.7 30803 3 26.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.06 96.6 0.702 3.6 2996
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3I79 1.98 30 30780 1556 98.17 0.195 0.193 0.2077 0.245 0.2551 RANDOM 26.071
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] 0.45 0.24 -0.62 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.764 r_dihedral_angle_4_deg 16.923 r_dihedral_angle_3_deg 13.537 r_dihedral_angle_1_deg 4.659 r_scangle_it 4.492 r_scbond_it 2.85 r_mcangle_it 2.331 r_mcbond_it 1.385 r_angle_refined_deg 0.978 r_angle_other_deg 0.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.764 r_dihedral_angle_4_deg 16.923 r_dihedral_angle_3_deg 13.537 r_dihedral_angle_1_deg 4.659 r_scangle_it 4.492 r_scbond_it 2.85 r_mcangle_it 2.331 r_mcbond_it 1.385 r_angle_refined_deg 0.978 r_angle_other_deg 0.762 r_mcbond_other 0.383 r_chiral_restr 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3712 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 24
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling