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Crystal structure of Cryptosporidium parvum calcium dependent protein kinase cgd7_1840 in presence of indirubin E804
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QG5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 18% PEG 3350, 0.1 M NH4SO4, 0.1 M NaCacodylate, 5 mM Indirubin E804, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.38 48.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.316 α = 90 b = 82.864 β = 111.61 c = 62.151 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray IMAGE PLATE RIGAKU RAXIS IV++ 2008-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.84 50 99.2 0.054 0.032 3.7 25859 25653 26.754
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 1.91 95.7 0.606 0.53 2.5 3.5 2464
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2qg5 1.84 57.83 25825 25653 1303 99.33 0.189 0.189 0.187 0.1846 0.23 0.2286 RANDOM 27.471
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 -0.42 0.57 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.341 r_dihedral_angle_4_deg 17.156 r_dihedral_angle_3_deg 13.207 r_dihedral_angle_1_deg 5.278 r_scangle_it 2.788 r_scbond_it 1.704 r_angle_refined_deg 1.501 r_mcangle_it 1.278 r_mcbond_it 0.812 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.341 r_dihedral_angle_4_deg 17.156 r_dihedral_angle_3_deg 13.207 r_dihedral_angle_1_deg 5.278 r_scangle_it 2.788 r_scbond_it 1.704 r_angle_refined_deg 1.501 r_mcangle_it 1.278 r_mcbond_it 0.812 r_nbtor_refined 0.302 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.184 r_xyhbond_nbd_refined 0.156 r_symmetry_hbond_refined 0.155 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2186 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 51
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling