3OVZ

Cathepsin K in complex with a covalent inhibitor with a ketoamide warhead


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
12980 mM NaAcetate pH=4.0, 0.3 M NaCl, 20% PEG4000, 0.2 M (NH4)2SO4, pH=2.9, 4% Methanol, Cryoprotectant composition:20% PEG4000, 0.1M (NH4)2SO4 pH=2.9, 4% Methanol, 20% PEG 400, pH 5, cocrystallization, hanging drop, temperature 398K
Crystal Properties
Matthews coefficientSolvent content
2.0238.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.741α = 90
b = 55.741β = 90
c = 128.916γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2008-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.0255.7410014051
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)
12.022.091000.72

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTIn-house cathepsin K structure2.0251.161399169899.70.2470.2440.30835.26
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]
0.990.99-1.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.592
r_dihedral_angle_3_deg18.138
r_dihedral_angle_4_deg13.198
r_dihedral_angle_1_deg6.198
r_scangle_it2.502
r_scbond_it1.891
r_angle_refined_deg1.785
r_mcangle_it1.106
r_angle_other_deg1.052
r_mcbond_it0.917
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.592
r_dihedral_angle_3_deg18.138
r_dihedral_angle_4_deg13.198
r_dihedral_angle_1_deg6.198
r_scangle_it2.502
r_scbond_it1.891
r_angle_refined_deg1.785
r_mcangle_it1.106
r_angle_other_deg1.052
r_mcbond_it0.917
r_symmetry_vdw_other0.3
r_symmetry_vdw_refined0.276
r_symmetry_hbond_refined0.257
r_nbd_refined0.215
r_nbd_other0.211
r_nbtor_refined0.187
r_mcbond_other0.171
r_xyhbond_nbd_refined0.16
r_chiral_restr0.104
r_nbtor_other0.092
r_bond_refined_d0.016
r_gen_planes_refined0.006
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 Atoms1637
Nucleic Acid Atoms
Solvent Atoms79
Heterogen Atoms40

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling