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Structure of cathepsin B1 from Schistosoma mansoni in complex with K11777 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QSD PDB ENTRY 3QSD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293 reservoir: 0.2 M Ammonium Acetate pH6.2, 0.1 M Na Citrate, 30% PEG 1500,
protein buffer and concentration: 10 mM Na-acetate pH 5.5,
Cpr = 6 mg/ml, protein: reservoir = 1:1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.36 47.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.633 α = 90 b = 103.121 β = 90 c = 100.697 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 210r mirrors 2009-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9791 APS 19-BM
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 2.5 50 99.8 0.062 21.7 6 24266 24218 69.1
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 2.5 2.65 99.5 0.669 1.85 5.6 1184
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 (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 3QSD 2.64 36.32 23187 22916 1236 98.83 0.20815 0.20462 0.2047 0.27142 0.2687 RANDOM 41.508
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] -0.22 0.59 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.74 r_dihedral_angle_4_deg 21.363 r_dihedral_angle_3_deg 17.835 r_dihedral_angle_1_deg 5.878 r_scangle_it 1.491 r_angle_refined_deg 1.287 r_scbond_it 0.937 r_mcangle_it 0.588 r_mcbond_it 0.348 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.74 r_dihedral_angle_4_deg 21.363 r_dihedral_angle_3_deg 17.835 r_dihedral_angle_1_deg 5.878 r_scangle_it 1.491 r_angle_refined_deg 1.287 r_scbond_it 0.937 r_mcangle_it 0.588 r_mcbond_it 0.348 r_nbtor_refined 0.309 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.198 r_xyhbond_nbd_refined 0.143 r_symmetry_hbond_refined 0.139 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5953 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 123
Software Software Software Name Purpose HKL-3000 data collection REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling REFMAC phasing