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Structure of human cathepsin K in complex with the acrylamide inhibitor Gu3110
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NXM D_1292114281
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 1.98 38.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.366 α = 90 b = 71.819 β = 90 c = 80.771 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 2020-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 40.39 93 0.14 0.168 0.093 0.996 20.94 5.6 19606
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 95.3 1.495 0.941 0.469 3.6
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-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE D_1292114281 1.8 35.226 18051 910 99.575 0.176 0.1764 0.1746 0.2094 0.1891 RANDOM 23.293
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] 1.258 -1.408 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.682 r_dihedral_angle_4_deg 16.861 r_dihedral_angle_3_deg 12.995 r_dihedral_angle_other_3_deg 9.873 r_dihedral_angle_1_deg 6.132 r_lrange_it 5.682 r_lrange_other 5.681 r_scangle_it 4.37 r_scangle_other 4.368 r_scbond_it 2.891
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.682 r_dihedral_angle_4_deg 16.861 r_dihedral_angle_3_deg 12.995 r_dihedral_angle_other_3_deg 9.873 r_dihedral_angle_1_deg 6.132 r_lrange_it 5.682 r_lrange_other 5.681 r_scangle_it 4.37 r_scangle_other 4.368 r_scbond_it 2.891 r_scbond_other 2.89 r_mcangle_other 2.786 r_mcangle_it 2.778 r_mcbond_it 1.964 r_mcbond_other 1.941 r_angle_refined_deg 1.656 r_angle_other_deg 1.386 r_symmetry_nbd_refined 0.203 r_nbd_refined 0.197 r_symmetry_nbd_other 0.185 r_xyhbond_nbd_refined 0.176 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.167 r_nbd_other 0.144 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1652 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing