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Crystal Structure of Human Cathepsin B with a L-peptide substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AY2 single chain without ligand
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 1.6 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10% v/v 1,4-Dioxane
Crystal Properties Matthews coefficient Solvent content 1.99 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.617 α = 90 b = 75.096 β = 90 c = 97.642 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 AGILENT ATLAS CCD 2025-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE Cu FINE FOCUS 1.50004
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 1.5 28.4 99.64 0.992 23.98 4.6 36878
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 1.5 1.554 97.68 0.788 2.4 3
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 1.5 28.37 35094 1784 99.64 0.17973 0.17824 0.1801 0.20882 0.2096 RANDOM 10.087
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] -0.05 -0.83 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.901 r_dihedral_angle_2_deg 11.613 r_dihedral_angle_1_deg 6.979 r_long_range_B_refined 4.291 r_long_range_B_other 4.228 r_scangle_other 3.112 r_mcangle_it 2.046 r_mcangle_other 2.046 r_scbond_it 1.98 r_scbond_other 1.979
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.901 r_dihedral_angle_2_deg 11.613 r_dihedral_angle_1_deg 6.979 r_long_range_B_refined 4.291 r_long_range_B_other 4.228 r_scangle_other 3.112 r_mcangle_it 2.046 r_mcangle_other 2.046 r_scbond_it 1.98 r_scbond_other 1.979 r_angle_refined_deg 1.732 r_mcbond_it 1.325 r_mcbond_other 1.318 r_angle_other_deg 0.623 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 1981 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing HKL-3000 data scaling