☰ Navigation Tabs
Cathepsin K covalently bound to a cyano-pyrimidine inhibitor with improved selectivity over hERG
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 3.9 298 8% PEG 4K, 0.2 M Ammonium Sulfate pH=3.9, 4%
Methanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.04 39.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.695 α = 90 b = 48.967 β = 90 c = 103.958 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 IMAGE PLATE MARRESEARCH 2006-06-15 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) 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 1.8 51.988 100 0.053 10838 10838 1.9 1.9
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) 1.8 1.86 16.1 0.133 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 1.8 51.988 1.9 10322 516 58.59 0.15512 0.15201 0.1548 0.2168 0.2147 RANDOM 12.813
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] -0.19 0.12 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.565 r_dihedral_angle_3_deg 17.069 r_dihedral_angle_4_deg 16.694 r_dihedral_angle_1_deg 5.396 r_scangle_it 2.469 r_scbond_it 1.787 r_angle_refined_deg 1.431 r_mcangle_it 1.035 r_angle_other_deg 0.904 r_mcbond_it 0.842
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.565 r_dihedral_angle_3_deg 17.069 r_dihedral_angle_4_deg 16.694 r_dihedral_angle_1_deg 5.396 r_scangle_it 2.469 r_scbond_it 1.787 r_angle_refined_deg 1.431 r_mcangle_it 1.035 r_angle_other_deg 0.904 r_mcbond_it 0.842 r_symmetry_vdw_other 0.295 r_nbd_refined 0.222 r_nbd_other 0.203 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.172 r_mcbond_other 0.168 r_symmetry_vdw_refined 0.157 r_symmetry_hbond_refined 0.148 r_chiral_restr 0.085 r_nbtor_other 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 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 1649 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 26
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling