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Cathepsin K in complex with a non-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 8.4 26% PEG 4000, 0.1M Tris, 0.2M LiSO4, 15% PEG 400, pH 8.4, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.14 42.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.814 α = 90 b = 55.814 β = 90 c = 129.115 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 2005-12-12 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 1.49 51.23 81.8 0.132 8 10.26 28061 28061 16.5
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 1.49 1.54 19.7 0.132 0.7 1.78
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) 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 1.49 42.22 1 28061 26506 1398 81.93 0.23863 0.23554 0.2379 0.29878 0.2979 RANDOM 22.048
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] 0.61 0.61 -1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.293 r_dihedral_angle_3_deg 16.253 r_dihedral_angle_4_deg 8.927 r_dihedral_angle_1_deg 6.313 r_scangle_it 3.443 r_scbond_it 2.545 r_angle_refined_deg 1.852 r_mcangle_it 1.43 r_mcbond_it 1.229 r_angle_other_deg 1.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.293 r_dihedral_angle_3_deg 16.253 r_dihedral_angle_4_deg 8.927 r_dihedral_angle_1_deg 6.313 r_scangle_it 3.443 r_scbond_it 2.545 r_angle_refined_deg 1.852 r_mcangle_it 1.43 r_mcbond_it 1.229 r_angle_other_deg 1.118 r_symmetry_hbond_refined 0.275 r_mcbond_other 0.257 r_symmetry_vdw_other 0.255 r_xyhbond_nbd_refined 0.194 r_nbd_other 0.193 r_nbd_refined 0.19 r_nbtor_refined 0.176 r_symmetry_vdw_refined 0.141 r_chiral_restr 0.098 r_nbtor_other 0.093 r_bond_refined_d 0.021 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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 1649 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 57
Software Software Software Name Purpose CrystalClear data collection REFMAC refinement CrystalClear data reduction CrystalClear data scaling