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Cathepsin K covalently bound to a 2-cyano pyrimidine inhibitor with a benzyl P3 group.
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 VAPOR DIFFUSION, HANGING DROP 8.4 298 Cocrystallization. Protein solution: 20 mM NaAcetate pH 4.0, 0.2 M NaCl. Crystallization condition: 32% PEG 4K, 0.1 M Tris pH 8.4, 0.2 M LiSO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.36 47.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.504 α = 90 b = 62.504 β = 90 c = 113.478 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 298 CCD ADSC QUANTUM 4 2007-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.93300 ESRF ID14-2
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 1.65 42 100 25977 25977
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 In house cathepsin K structure 1.65 42 25977 1381 100 0.16995 0.1684 0.1747 0.19849 0.208 RANDOM 12.953
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.402 r_dihedral_angle_4_deg 16.977 r_dihedral_angle_3_deg 12.415 r_dihedral_angle_1_deg 5.269 r_sphericity_free 4.712 r_scangle_it 3.16 r_scbond_it 2.475 r_rigid_bond_restr 2.207 r_sphericity_bonded 2.033 r_mcangle_it 1.434
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.402 r_dihedral_angle_4_deg 16.977 r_dihedral_angle_3_deg 12.415 r_dihedral_angle_1_deg 5.269 r_sphericity_free 4.712 r_scangle_it 3.16 r_scbond_it 2.475 r_rigid_bond_restr 2.207 r_sphericity_bonded 2.033 r_mcangle_it 1.434 r_angle_refined_deg 1.283 r_mcbond_it 1.263 r_angle_other_deg 0.849 r_mcbond_other 0.372 r_symmetry_vdw_other 0.291 r_nbd_refined 0.2 r_nbd_other 0.184 r_nbtor_refined 0.179 r_symmetry_hbond_refined 0.162 r_symmetry_vdw_refined 0.141 r_xyhbond_nbd_refined 0.128 r_nbtor_other 0.085 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1649 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 46
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement CrystalClear data reduction SCALA data scaling