2XU4

CATHEPSIN L WITH A NITRILE INHIBITOR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherIN HOUSE STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
13.50.1 M CITRIC ACID PH 3.5, 25 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.1342.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.362α = 90
b = 85.362β = 90
c = 50.212γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2010-08-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
11.1501000.0712.110.1484484-315.5
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)
11.11.191000.771.0410.15

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 STRUCTURE1.1242.6872914381495.80.141710.140360.16725RANDOM18.523
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]
-1.3-0.65-1.31.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.446
r_dihedral_angle_4_deg15.926
r_dihedral_angle_3_deg11.534
r_sphericity_free11.255
r_sphericity_bonded6.923
r_dihedral_angle_1_deg5.58
r_rigid_bond_restr4.677
r_angle_refined_deg1.452
r_angle_other_deg0.875
r_chiral_restr0.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.446
r_dihedral_angle_4_deg15.926
r_dihedral_angle_3_deg11.534
r_sphericity_free11.255
r_sphericity_bonded6.923
r_dihedral_angle_1_deg5.58
r_rigid_bond_restr4.677
r_angle_refined_deg1.452
r_angle_other_deg0.875
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1674
Nucleic Acid Atoms
Solvent Atoms252
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SADABSdata scaling
PHASERphasing