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Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with bumped kinase inhibitor RM-1-95
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I7B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 24% PEG 3350, 0.25 M ammonium citrate, 5 mM DTT, 2.3 mM RM-1-95; cryoprotected by quick dip into well soln + final conc. (4.5% SGPP buffer, 9% ethylene glycol, 2 mM RM-1-95), pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.04 39.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.523 α = 90 b = 72.754 β = 98.88 c = 66.024 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 ADSC QUANTUM 315r 2009-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.976 SSRL BL7-1
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 2.1 50 99.9 0.094 6.6 3.8 26020 5 41.3
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) 2.1 2.18 99.9 0.799 1.1 3.8 2590
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 FOURIER SYNTHESIS THROUGHOUT 3i7b 2.1 39.45 26002 1325 99.88 0.196 0.193 0.1987 0.242 0.2442 RANDOM 50.291
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] -0.1 0.87 0.41 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.67 r_dihedral_angle_4_deg 19.377 r_dihedral_angle_3_deg 14.053 r_dihedral_angle_1_deg 5.182 r_scangle_it 5.099 r_scbond_it 3.509 r_mcangle_it 2.747 r_mcbond_it 1.754 r_angle_refined_deg 1.124 r_angle_other_deg 0.801
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.67 r_dihedral_angle_4_deg 19.377 r_dihedral_angle_3_deg 14.053 r_dihedral_angle_1_deg 5.182 r_scangle_it 5.099 r_scbond_it 3.509 r_mcangle_it 2.747 r_mcbond_it 1.754 r_angle_refined_deg 1.124 r_angle_other_deg 0.801 r_mcbond_other 0.544 r_chiral_restr 0.062 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3613 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 36
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing