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Structure of the activation intermediate of cathepsin K in complex with the azadipeptide nitrile inhibitor Gu1303
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NXM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 290 10% PEG 8000, 20% ethylene glycol, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine HCl, 0.02 M DL-serine, 0.1M MES/imidazole pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.07 40.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.214 α = 90 b = 103.214 β = 90 c = 54.985 γ = 90
Symmetry Space Group P 43 21 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 PILATUS3 6M 2018-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 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 1.9 46.2 99.8 0.111 0.118 0.998 13.34 7.894 23911 27.475
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 1.9 2.02 99.3 0.63 0.677 0.853 2.86 7.494
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 7NXM 1.9 46.2 22715 1196 99.84 0.1667 0.1643 0.1752 0.2116 0.2226 RANDOM 23.299
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] -0.4 -0.4 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.206 r_dihedral_angle_4_deg 21.572 r_dihedral_angle_3_deg 14.072 r_dihedral_angle_1_deg 5.682 r_angle_refined_deg 1.503 r_angle_other_deg 1.413 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.206 r_dihedral_angle_4_deg 21.572 r_dihedral_angle_3_deg 14.072 r_dihedral_angle_1_deg 5.682 r_angle_refined_deg 1.503 r_angle_other_deg 1.413 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2209 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction PDB_EXTRACT data extraction XDS data scaling BUCCANEER phasing