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Cathepsin K in complex with a selective 2-cyano-pyrimidine inhibitor
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 2.9 34% PEG 4000, 0.2M ammonium sulphate pH 2.9, 4% methanol
, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.15 42.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.069 α = 90 b = 56.069 β = 90 c = 128.829 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 CCD ADSC QUANTUM 4 2005-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.51 37.89 70.3 0.101 6.7 2.79 23303 23303 14.7
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 1.51 1.56 9.2 0.101 0.7 1.13
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 1.51 28.03 22075 1167 70.13 0.24256 0.2394 0.2393 0.30616 0.302 RANDOM 17.269
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] 0.48 0.48 -0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.128 r_dihedral_angle_3_deg 14.36 r_dihedral_angle_4_deg 9.928 r_dihedral_angle_1_deg 6.122 r_scangle_it 2.519 r_scbond_it 1.837 r_angle_refined_deg 1.508 r_mcangle_it 1.03 r_angle_other_deg 1.003 r_mcbond_it 0.869
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.128 r_dihedral_angle_3_deg 14.36 r_dihedral_angle_4_deg 9.928 r_dihedral_angle_1_deg 6.122 r_scangle_it 2.519 r_scbond_it 1.837 r_angle_refined_deg 1.508 r_mcangle_it 1.03 r_angle_other_deg 1.003 r_mcbond_it 0.869 r_symmetry_vdw_other 0.247 r_nbd_refined 0.211 r_symmetry_hbond_refined 0.21 r_symmetry_vdw_refined 0.205 r_nbd_other 0.196 r_mcbond_other 0.19 r_xyhbond_nbd_refined 0.18 r_nbtor_refined 0.174 r_chiral_restr 0.087 r_nbtor_other 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 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 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 203 Heterogen Atoms 34
Software Software Software Name Purpose CrystalClear data collection REFMAC refinement CrystalClear data reduction CrystalClear data scaling