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Human cathepsin B in complex with the carbamate inhibitor 7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IPP 2IPP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 0.1 M Sodium Acetate pH 5.5, 20% PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.1 41.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.75 α = 90 b = 81.55 β = 90 c = 93.46 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 2021-11-10 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) 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 1.45 46.73 98.8 0.176 0.183 0.998 11.36 12.968 42360 24.852
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 1.45 1.54 96.9 3.12 3.25 0.397 0.78 12.544
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 2IPP 1.45 46.73 40259 2101 98.82 0.1788 0.1773 0.1772 0.2081 0.2075 RANDOM 19.795
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] 0.79 -1.37 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.374 r_dihedral_angle_4_deg 23.196 r_dihedral_angle_3_deg 13.53 r_dihedral_angle_1_deg 7.045 r_angle_refined_deg 1.801 r_angle_other_deg 1.556 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.374 r_dihedral_angle_4_deg 23.196 r_dihedral_angle_3_deg 13.53 r_dihedral_angle_1_deg 7.045 r_angle_refined_deg 1.801 r_angle_other_deg 1.556 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1952 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction