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Human cathepsin B in complex with the carbamate inhibitor 31
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8B4T 8B4T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 0.1 M Sodium Acetate pH 5.5, 30% PEG 5000 MME
Crystal Properties Matthews coefficient Solvent content 2.09 41.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.573 α = 90 b = 81.565 β = 90 c = 93.52 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 1.7 46.76 99.9 0.247 0.257 0.997 9.34 12.9 26540 28.907
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 1.7 1.8 99.7 3.16 3.291 0.33 0.83 12.851
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 8B4T 1.7 46.76 25215 1328 99.9 0.1762 0.1747 0.1838 0.2051 0.2169 RANDOM 23.241
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] -0.22 -0.74 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.872 r_dihedral_angle_4_deg 20.003 r_dihedral_angle_3_deg 12.445 r_dihedral_angle_1_deg 7.038 r_angle_refined_deg 1.667 r_angle_other_deg 1.466 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.872 r_dihedral_angle_4_deg 20.003 r_dihedral_angle_3_deg 12.445 r_dihedral_angle_1_deg 7.038 r_angle_refined_deg 1.667 r_angle_other_deg 1.466 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1960 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction