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Crystal structure of human cathepsin S produced in insect cells in complex with ketoamide 13b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YYN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Cathepsin S (7 mg/ml) was mixed with an equal volume of reservoir and equilibrated against 20% (w/v) PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium citrate pH 4.6. Crystals were soaked with ketoamide 13b in the presence of 5% (v/v) DMSO.
Crystal Properties Matthews coefficient Solvent content 2.9 57.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.102 α = 90 b = 86.102 β = 90 c = 152.045 γ = 90
Symmetry Space Group P 41 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 EIGER2 X 16M 2024-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033190 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.15 47.52 91.1 0.083 0.999 15.22 11.7 353434
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 1.15 1.16 0.215
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.15 47.52 1.34 353348 3837 91.07 0.1514 0.1513 0.1517 0.1618 0.1612 16.47
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.2502 f_angle_d 0.7448 f_chiral_restr 0.0756 f_plane_restr 0.0061 f_bond_d 0.0042
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3403 Nucleic Acid Atoms Solvent Atoms 446 Heterogen Atoms 123
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing