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Peptide-Small Molecule Hybrids as Novel Selective Irreversible Cathepsin-K Inhibitors in Primary Osteoclasts and Human Lung Cancer Tissue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QBS none
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6 293 20 % PEG-3350, 0.2 M CaCl2
Crystal Properties Matthews coefficient Solvent content 2.83 56.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.37 α = 90 b = 74.37 β = 90 c = 336.42 γ = 120
Symmetry Space Group P 61 2 2
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 2022-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.92 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.99 38.52 99.9 0.127 0.94 12.6 35.5 38918 5.42 34.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.12 99.8 0.713 0.944 34.9
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 (All) 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 FOURIER SYNTHESIS NONE 1.99 38.52 38917 38917 100 0.1804 0.1804 0.1804 0.1812 0.2056 0.1787 NONE
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] -0.335 -0.131 -0.335 0.671
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3337 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 68
Software Software Software Name Purpose MAIN refinement XDS data reduction XDS data scaling FFT phasing