3O0U

Cathepsin K covalently bound to a cyano-pyrimidine inhibitor with improved selectivity over hERG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherIn-house cathepsin K structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3.92988% PEG 4K, 0.2 M Ammonium Sulfate pH=3.9, 4% Methanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0439.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.695α = 90
b = 48.967β = 90
c = 103.958γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMARRESEARCH2006-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.851.9881000.05310838108381.91.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.8616.10.1331.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTIn-house cathepsin K structure1.851.9881.91032251658.590.155120.152010.2168RANDOM12.813
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]
-0.190.120.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.565
r_dihedral_angle_3_deg17.069
r_dihedral_angle_4_deg16.694
r_dihedral_angle_1_deg5.396
r_scangle_it2.469
r_scbond_it1.787
r_angle_refined_deg1.431
r_mcangle_it1.035
r_angle_other_deg0.904
r_mcbond_it0.842
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.565
r_dihedral_angle_3_deg17.069
r_dihedral_angle_4_deg16.694
r_dihedral_angle_1_deg5.396
r_scangle_it2.469
r_scbond_it1.787
r_angle_refined_deg1.431
r_mcangle_it1.035
r_angle_other_deg0.904
r_mcbond_it0.842
r_symmetry_vdw_other0.295
r_nbd_refined0.222
r_nbd_other0.203
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.172
r_mcbond_other0.168
r_symmetry_vdw_refined0.157
r_symmetry_hbond_refined0.148
r_chiral_restr0.085
r_nbtor_other0.085
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms1649
Nucleic Acid Atoms
Solvent Atoms151
Heterogen Atoms26

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling