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Crystal Structure of cgd4_240 from cryptosporidium Parvum in complex with indirubin E804
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O9U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 10% Isopropanol
20% PEG 4000
0.1 M NaHepes 7.5
4 mM indirubin E804
20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.29 46.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.101 α = 90 b = 138.366 β = 90 c = 43.261 γ = 90
Symmetry Space Group P 21 21 2
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 300 mm CCD 2008-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.96749 APS 23-ID-D
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 2.65 50 99.4 0.189 0.117 13.083 6.7 24691 24543 47.77
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 2.65 2.74 95.7 0.801 0.591 1.77 5.1 2313
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 1o9u 2.65 35 24253 24140 1234 99.53 0.24 0.24 0.238 0.2356 0.295 0.2976 RANDOM 21.267
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] -1.51 2.34 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.47 r_dihedral_angle_4_deg 20.449 r_dihedral_angle_3_deg 18.136 r_dihedral_angle_1_deg 5.821 r_scangle_it 1.861 r_angle_refined_deg 1.396 r_scbond_it 1.148 r_mcangle_it 0.743 r_mcbond_it 0.422 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.47 r_dihedral_angle_4_deg 20.449 r_dihedral_angle_3_deg 18.136 r_dihedral_angle_1_deg 5.821 r_scangle_it 1.861 r_angle_refined_deg 1.396 r_scbond_it 1.148 r_mcangle_it 0.743 r_mcbond_it 0.422 r_nbtor_refined 0.314 r_symmetry_hbond_refined 0.262 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4965 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 78
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction