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Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with bumped kinase inhibitor NM-PP1
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, 0.18 M ammonium citrate, 4 mM NM-PP1; cryoprotected with 10% ethylene glycol, pH 6.5, sitting drop vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.02 39.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.243 α = 90 b = 72.851 β = 98.78 c = 65.713 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 0.97946 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 1.988 50 99.8 0.065 8.3 4.2 30350 5 29.7
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 1.988 2.06 98.1 0.741 1.9 4.1 2975
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3I79 1.988 50 30333 1536 99.77 0.194 0.192 0.228 0.2573 RANDOM 19.845
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] 0.34 0.78 0.67 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.84 r_dihedral_angle_4_deg 18.445 r_dihedral_angle_3_deg 12.534 r_dihedral_angle_1_deg 4.557 r_scangle_it 3.245 r_scbond_it 2.054 r_mcangle_it 1.724 r_mcbond_it 0.985 r_angle_refined_deg 0.878 r_angle_other_deg 0.749
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.84 r_dihedral_angle_4_deg 18.445 r_dihedral_angle_3_deg 12.534 r_dihedral_angle_1_deg 4.557 r_scangle_it 3.245 r_scbond_it 2.054 r_mcangle_it 1.724 r_mcbond_it 0.985 r_angle_refined_deg 0.878 r_angle_other_deg 0.749 r_mcbond_other 0.245 r_chiral_restr 0.05 r_bond_refined_d 0.006 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 3694 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 40
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