3KX1

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2.934% PEG 4000, 0.2M ammonium sulphate pH 2.9, 4% methanol , VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.1542.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.069α = 90
b = 56.069β = 90
c = 128.829γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 42005-03-15MSINGLE 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
11.5137.8970.30.1016.72.79233032330314.7
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)
11.511.569.20.1010.71.13

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 structure1.5128.0322075116770.130.242560.23940.30616RANDOM17.269
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]
0.480.48-0.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.128
r_dihedral_angle_3_deg14.36
r_dihedral_angle_4_deg9.928
r_dihedral_angle_1_deg6.122
r_scangle_it2.519
r_scbond_it1.837
r_angle_refined_deg1.508
r_mcangle_it1.03
r_angle_other_deg1.003
r_mcbond_it0.869
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.128
r_dihedral_angle_3_deg14.36
r_dihedral_angle_4_deg9.928
r_dihedral_angle_1_deg6.122
r_scangle_it2.519
r_scbond_it1.837
r_angle_refined_deg1.508
r_mcangle_it1.03
r_angle_other_deg1.003
r_mcbond_it0.869
r_symmetry_vdw_other0.247
r_nbd_refined0.211
r_symmetry_hbond_refined0.21
r_symmetry_vdw_refined0.205
r_nbd_other0.196
r_mcbond_other0.19
r_xyhbond_nbd_refined0.18
r_nbtor_refined0.174
r_chiral_restr0.087
r_nbtor_other0.085
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_gen_planes_other0.003
r_bond_other_d0.002
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 AtomsNumber
Protein Atoms1637
Nucleic Acid Atoms
Solvent Atoms203
Heterogen Atoms34

Software

Software
Software NamePurpose
CrystalCleardata collection
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling