2H7J

Crystal Structure of Cathepsin S in complex with a Nonpeptidic Inhibitor.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP527730% Peg-6000, 0.1M Lithium Chloride in Citrate Buffer pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.856.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.222α = 90
b = 85.222β = 90
c = 150.754γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-07-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.31.0ALS5.0.3

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
11.538.699.30.0730.07327.49245392453
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)
1.51.5395.30.6420.6422.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT2f1g1.538.68434584345450899.420.162350.161430.17969RANDOM12.293
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]
0.110.11-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.936
r_dihedral_angle_4_deg13.527
r_dihedral_angle_3_deg10.392
r_dihedral_angle_1_deg5.377
r_scangle_it2.729
r_scbond_it1.731
r_angle_refined_deg1.331
r_mcangle_it1.081
r_angle_other_deg0.723
r_mcbond_it0.699
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.936
r_dihedral_angle_4_deg13.527
r_dihedral_angle_3_deg10.392
r_dihedral_angle_1_deg5.377
r_scangle_it2.729
r_scbond_it1.731
r_angle_refined_deg1.331
r_mcangle_it1.081
r_angle_other_deg0.723
r_mcbond_it0.699
r_xyhbond_nbd_refined0.263
r_symmetry_vdw_refined0.21
r_nbd_refined0.2
r_symmetry_vdw_other0.192
r_nbtor_refined0.191
r_nbd_other0.177
r_symmetry_hbond_refined0.166
r_mcbond_other0.141
r_nbtor_other0.083
r_chiral_restr0.067
r_bond_refined_d0.015
r_gen_planes_refined0.004
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 Atoms3429
Nucleic Acid Atoms
Solvent Atoms549
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
CCP4data scaling