3KWZ

Cathepsin K in complex with a non-selective 2-cyano-pyrimidine inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.426% PEG 4000, 0.1M Tris, 0.2M LiSO4, 15% PEG 400, pH 8.4, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.1442.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.814α = 90
b = 55.814β = 90
c = 129.115γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 42005-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

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
11.4951.2381.80.132810.26280612806116.5
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)
11.491.5419.70.1320.71.78

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)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 structure1.4942.2212806126506139881.930.238630.235540.29878RANDOM22.048
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]
0.610.61-1.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.293
r_dihedral_angle_3_deg16.253
r_dihedral_angle_4_deg8.927
r_dihedral_angle_1_deg6.313
r_scangle_it3.443
r_scbond_it2.545
r_angle_refined_deg1.852
r_mcangle_it1.43
r_mcbond_it1.229
r_angle_other_deg1.118
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.293
r_dihedral_angle_3_deg16.253
r_dihedral_angle_4_deg8.927
r_dihedral_angle_1_deg6.313
r_scangle_it3.443
r_scbond_it2.545
r_angle_refined_deg1.852
r_mcangle_it1.43
r_mcbond_it1.229
r_angle_other_deg1.118
r_symmetry_hbond_refined0.275
r_mcbond_other0.257
r_symmetry_vdw_other0.255
r_xyhbond_nbd_refined0.194
r_nbd_other0.193
r_nbd_refined0.19
r_nbtor_refined0.176
r_symmetry_vdw_refined0.141
r_chiral_restr0.098
r_nbtor_other0.093
r_bond_refined_d0.021
r_gen_planes_refined0.007
r_bond_other_d0.001
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 Atoms153
Heterogen Atoms57

Software

Software
Software NamePurpose
CrystalCleardata collection
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling