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CDPK1 from Neospora caninum in complex with inhibitor RM-1-132
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4M97 PDB ENTRY 4M97
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 protein solution: 25 mM HEPES pH 7.0, 0.5 M NaCl, 5% glycerol, 5 mM DTT, 20 mM EGTA, 3mg/ml protein, 0.2 mM RM-1-132, 1% DMSO; crystallization buffer: 30% PEG 3350, 0.2 M ammonium citrate, 0.1 M BisTris pH 5.3, 5 mM DTT, vapor diffusion, sitting drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.06 40.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.22 α = 90 b = 72.53 β = 99.28 c = 65.65 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 DECTRIS PILATUS 6M 2013-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97939 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 3 47.59 89.1 0.376 3.6 2.8 8027
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 3 3.21 89.7 0.018 1 2.7 1432
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 PDB ENTRY 4M97 3 47.63 7097 328 78.52 0.2538 0.2526 0.2545 0.2793 0.2809 RANDOM 73.6112
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] -2.98 0.4 0.97 1.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.389 r_dihedral_angle_3_deg 16.412 r_dihedral_angle_4_deg 15.291 r_dihedral_angle_1_deg 5.533 r_mcangle_it 2.602 r_mcbond_it 1.509 r_mcbond_other 1.507 r_angle_refined_deg 1.43 r_angle_other_deg 0.801 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.389 r_dihedral_angle_3_deg 16.412 r_dihedral_angle_4_deg 15.291 r_dihedral_angle_1_deg 5.533 r_mcangle_it 2.602 r_mcbond_it 1.509 r_mcbond_other 1.507 r_angle_refined_deg 1.43 r_angle_other_deg 0.801 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3670 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 30
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection MOSFLM data reduction