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Structure of cathepsin B1 from Schistosoma mansoni in complex with K11017 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 pH 6.2, 0.1 M Na citrate, 30%(v/w) PEG 1500, protein buffer and concentration: 10 mM Na acetate, pH 5.5, Cpr = 2.5 mg/ml, protein: reservoir: 1:1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.08 40.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.092 α = 90 b = 79.528 β = 90 c = 90.269 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 1.8 50 99.8 0.105 18.4 6.8 22940 22894 13.2
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 1.8 1.83 98 0.479 2.3 3.7 1134
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 3QSD 1.8 29.84 21744 21548 1162 99.21 0.176 0.16958 0.16614 0.1668 0.23624 0.2371 RANDOM 14.087
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] -0.18 -0.07 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.337 r_dihedral_angle_4_deg 15.311 r_dihedral_angle_3_deg 12.42 r_dihedral_angle_1_deg 5.816 r_scangle_it 2.604 r_scbond_it 1.74 r_angle_refined_deg 1.268 r_mcangle_it 0.976 r_mcbond_it 0.642 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.337 r_dihedral_angle_4_deg 15.311 r_dihedral_angle_3_deg 12.42 r_dihedral_angle_1_deg 5.816 r_scangle_it 2.604 r_scbond_it 1.74 r_angle_refined_deg 1.268 r_mcangle_it 0.976 r_mcbond_it 0.642 r_nbtor_refined 0.311 r_nbd_refined 0.215 r_symmetry_hbond_refined 0.184 r_symmetry_vdw_refined 0.172 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 1998 Nucleic Acid Atoms Solvent Atoms 536 Heterogen Atoms 45
Software Software Software Name Purpose HKL-3000 data collection REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling REFMAC phasing