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Cathepsin K in complex with a covalent inhibitor with a ketoamide warhead
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other In-house cathepsin K structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 298 0 mM NaAcetate pH=4.0, 0.3 M NaCl, 20% PEG4000, 0.2 M (NH4)2SO4, pH=2.9, 4% Methanol, Cryoprotectant composition:20%
PEG4000, 0.1M (NH4)2SO4 pH=2.9, 4% Methanol, 20% PEG 400, pH 5, cocrystallization, hanging drop, temperature 398K
Crystal Properties Matthews coefficient Solvent content 2.02 38.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.741 α = 90 b = 55.741 β = 90 c = 128.916 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 IMAGE PLATE RIGAKU RAXIS IV 2008-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.02 55.74 100 14051
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.02 2.09 100 0.7 2
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT In-house cathepsin K structure 2.02 51.16 13991 698 99.7 0.247 0.244 0.2437 0.308 0.2993 35.26
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] 0.99 0.99 -1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.592 r_dihedral_angle_3_deg 18.138 r_dihedral_angle_4_deg 13.198 r_dihedral_angle_1_deg 6.198 r_scangle_it 2.502 r_scbond_it 1.891 r_angle_refined_deg 1.785 r_mcangle_it 1.106 r_angle_other_deg 1.052 r_mcbond_it 0.917
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.592 r_dihedral_angle_3_deg 18.138 r_dihedral_angle_4_deg 13.198 r_dihedral_angle_1_deg 6.198 r_scangle_it 2.502 r_scbond_it 1.891 r_angle_refined_deg 1.785 r_mcangle_it 1.106 r_angle_other_deg 1.052 r_mcbond_it 0.917 r_symmetry_vdw_other 0.3 r_symmetry_vdw_refined 0.276 r_symmetry_hbond_refined 0.257 r_nbd_refined 0.215 r_nbd_other 0.211 r_nbtor_refined 0.187 r_mcbond_other 0.171 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.104 r_nbtor_other 0.092 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1637 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 40
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement d*TREK data reduction d*TREK data scaling