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Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1517
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4M84 PDB entry 4M84
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 24% PEG 3350, 0.275 M ammonium citrate, 5 mM DTT, 2 mM UW1517, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.08 40.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.27 α = 90 b = 72.631 β = 102.36 c = 67.2 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 PIXEL PSI PILATUS 6M 2013-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.0332 SSRL BL12-2
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 2.4 48.7 95.5 0.155 7.5 3.1 17101
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 2.4 2.49 96.7 0.019 1.4 3.1
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 PDB entry 4M84 2.4 48.7 16218 859 95.63 0.19028 0.1873 0.1909 0.24795 0.2451 RANDOM 60.134
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] 0.56 1.8 -2.55 1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.516 r_dihedral_angle_4_deg 19.839 r_dihedral_angle_3_deg 16.848 r_dihedral_angle_1_deg 6.147 r_mcangle_it 2.759 r_scbond_it 2.314 r_mcbond_it 1.696 r_mcbond_other 1.695 r_angle_refined_deg 1.411 r_angle_other_deg 0.782
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.516 r_dihedral_angle_4_deg 19.839 r_dihedral_angle_3_deg 16.848 r_dihedral_angle_1_deg 6.147 r_mcangle_it 2.759 r_scbond_it 2.314 r_mcbond_it 1.696 r_mcbond_other 1.695 r_angle_refined_deg 1.411 r_angle_other_deg 0.782 r_chiral_restr 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3691 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 26
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection MOSFLM data reduction