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Structure of human cathepsin K in complex with the selective activity-based probe Gu3416
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TDI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 Composition of reservoir solution was 0.1 M MES/imidazole buffer, containing: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 0.03 M of each NPS (a mix containing sodium nitrate, disodium hydrogen phosphate and ammonium sulfate) additives, pH 6.5.
Morpheus C4 condition
Crystal Properties Matthews coefficient Solvent content 1.963 37.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.045 α = 90 b = 71.677 β = 90 c = 80.856 γ = 90
Symmetry Space Group P 2 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 300K 2020-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.541870
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.72 50 85.7 0.061 0.079 0.05 0.996 27.18 3.8 17548
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.75 14.8 0.423 0.598 0.423 0.678 1.4 1.3
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 (All) 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 5TDI 1.72 35.86 17510 895 85.34 0.161 0.1602 0.1608 0.1784 0.1787 RANDOM 17.819
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] 0.356 -1.202 0.846
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.746 r_dihedral_angle_4_deg 17.225 r_dihedral_angle_other_3_deg 13.112 r_dihedral_angle_3_deg 12.423 r_dihedral_angle_1_deg 5.896 r_lrange_it 5.28 r_lrange_other 5.14 r_scangle_it 3.85 r_scangle_other 3.849 r_scbond_it 2.579
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.746 r_dihedral_angle_4_deg 17.225 r_dihedral_angle_other_3_deg 13.112 r_dihedral_angle_3_deg 12.423 r_dihedral_angle_1_deg 5.896 r_lrange_it 5.28 r_lrange_other 5.14 r_scangle_it 3.85 r_scangle_other 3.849 r_scbond_it 2.579 r_scbond_other 2.578 r_mcangle_other 2.38 r_mcangle_it 2.377 r_mcbond_it 1.675 r_mcbond_other 1.661 r_angle_refined_deg 1.633 r_angle_other_deg 1.465 r_symmetry_xyhbond_nbd_refined 0.223 r_nbd_refined 0.209 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.175 r_nbd_other 0.167 r_xyhbond_nbd_refined 0.153 r_symmetry_nbd_refined 0.141 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1652 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PDB_EXTRACT data extraction MOLREP phasing