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Structure of cathepsin B1 from Schistosoma mansoni (SmCB1) in complex with an azanitrile inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S3Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 293 180 mM ammonium acetate, 80 mM sodium citrate, 27% PEG 1 500, pH 6.1
c (protein)= 4 mg/mL
ratio protein:reservoir = 1:1
cryocooled in mother liquor
Crystal Properties Matthews coefficient Solvent content 2.07 40.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.934 α = 90 b = 78.965 β = 90 c = 89.954 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 PIXEL DECTRIS PILATUS 6M 2015-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.29 44.98 98.9 0.052 0.062 0.999 13.53 3.24 58937 16.587
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.29 1.37 98.4 0.404 0.483 0.785 2.76 3.276
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3S3Q 1.29 44.98 57789 1147 98.9 0.1213 0.1206 0.1201 0.1571 0.1559 RANDOM 14.74
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] -0.53 0.19 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.386 r_sphericity_free 31.025 r_dihedral_angle_4_deg 12.232 r_dihedral_angle_3_deg 11.415 r_sphericity_bonded 9.927 r_dihedral_angle_1_deg 6.113 r_rigid_bond_restr 2.991 r_angle_refined_deg 1.552 r_angle_other_deg 0.875 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.386 r_sphericity_free 31.025 r_dihedral_angle_4_deg 12.232 r_dihedral_angle_3_deg 11.415 r_sphericity_bonded 9.927 r_dihedral_angle_1_deg 6.113 r_rigid_bond_restr 2.991 r_angle_refined_deg 1.552 r_angle_other_deg 0.875 r_chiral_restr 0.108 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1998 Nucleic Acid Atoms Solvent Atoms 408 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MOLREP phasing