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Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1455
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SX9 PDB ENTRY 3SX9
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 UW1455, pH 7.5, vapor diffusion, sitting drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.07 40.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.12 α = 90 b = 73.18 β = 99.77 c = 66.01 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 2013-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.127 SSRL BL14-1
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 1.998 48.673 94.6 0.058 10 3.7 28948 37.3
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 3SX9 1.998 48.67 28905 1448 94.19 0.201 0.198 0.2035 0.257 0.2543 RANDOM 54.6328
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] -0.87 0.56 0.58 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.516 r_dihedral_angle_3_deg 16.781 r_dihedral_angle_4_deg 16.212 r_dihedral_angle_1_deg 5.67 r_mcangle_it 2.983 r_mcbond_it 1.987 r_mcbond_other 1.987 r_angle_refined_deg 1.434 r_angle_other_deg 0.794 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.516 r_dihedral_angle_3_deg 16.781 r_dihedral_angle_4_deg 16.212 r_dihedral_angle_1_deg 5.67 r_mcangle_it 2.983 r_mcbond_it 1.987 r_mcbond_other 1.987 r_angle_refined_deg 1.434 r_angle_other_deg 0.794 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3698 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 23
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection MOSFLM data reduction