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Structure of cathepsin B1 from Schistosoma mansoni (SmCB1) in complex with a carborane inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4I07
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293 200 mM ammonium acetate, 100 mM sodium citrate, 30% PEG 1 500, 2 mM 2-mercaptoethanol, pH 6.2
c (protein)= 5 mg/mL
ratio protein:reservoir = 1:1
cryocooled in reservoir solution supplemented with 30% PEG 300, 1.75 mM DTT, 0.07 mM carborane inhibitor 2-oC
Crystal Properties Matthews coefficient Solvent content 2.31 46.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.726 α = 90 b = 81.726 β = 90 c = 102.091 γ = 120
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 2019-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.2 50 99.8 0.985 5.21 5.861 38651
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.33 0.352
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MOLECULAR REPLACEMENT THROUGHOUT 2.2 41.4 36677 1972 99.8 0.2044 0.20195 0.2047 0.25024 0.2519 RANDOM 38.734
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] 11.13 11.13 -22.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.12 r_dihedral_angle_4_deg 19.206 r_dihedral_angle_3_deg 13 r_long_range_B_refined 6.594 r_long_range_B_other 6.594 r_dihedral_angle_1_deg 5.896 r_scangle_other 4.835 r_mcangle_it 4.469 r_mcangle_other 4.469 r_angle_other_deg 3.375
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.12 r_dihedral_angle_4_deg 19.206 r_dihedral_angle_3_deg 13 r_long_range_B_refined 6.594 r_long_range_B_other 6.594 r_dihedral_angle_1_deg 5.896 r_scangle_other 4.835 r_mcangle_it 4.469 r_mcangle_other 4.469 r_angle_other_deg 3.375 r_scbond_it 3.32 r_scbond_other 3.32 r_mcbond_it 3.179 r_mcbond_other 3.175 r_angle_refined_deg 1.445 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_bond_other_d 0.012 r_gen_planes_refined 0.007 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5994 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing