1ATK

CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH THE COVALENT INHIBITOR E-64


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 9PAPPDB ENTRY 9PAP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.2PROTEIN CRYSTALLIZED FROM 10% PEG 8000, 0.1 M NA/K PHOSPHATE AT PH 6.2 CONTAINING 0.2 M NACL AT ROOM TEMPERATURE BY VAPOR DIFFUSION., vapor diffusion
Crystal Properties
Matthews coefficientSolvent content
2.143

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.4α = 90
b = 50.7β = 90
c = 104.9γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray287AREA DETECTORSIEMENSMONOCHROMATOR1995-10-25M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODESIEMENS

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.225950.0950.095143.2104182
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.22.34800.190.192.942.3

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 9PAP2.27210052106184.70.2150.2150.31RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d22.8
x_angle_deg1.51
x_improper_angle_d1.1
x_bond_d0.007
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d22.8
x_angle_deg1.51
x_improper_angle_d1.1
x_bond_d0.007
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1737
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms26

Software

Software
Software NamePurpose
XENGENdata collection
XENGENdata reduction
X-PLORmodel building
X-PLORrefinement
XENGENdata scaling
X-PLORphasing