2YJ2

CATHEPSIN L WITH A NITRILE INHIBITOR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XU4PDB ENTRY 2XU4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.1M BIS-TRIS PH 6.5, 25 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.9637.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.883α = 90
b = 57.147β = 90
c = 75.599γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-02-05MSINGLE 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
11.125096.10.06116.0574119-315.1
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)
11.121.2287.80.621.714.82

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2XU41.1545.5963343336793.540.147050.145350.17855RANDOM17.28
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]
-0.83-1.081.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.713
r_dihedral_angle_4_deg16.672
r_dihedral_angle_3_deg11.629
r_sphericity_free11.22
r_sphericity_bonded7.155
r_dihedral_angle_1_deg5.65
r_rigid_bond_restr2.127
r_angle_refined_deg1.36
r_angle_other_deg0.852
r_chiral_restr0.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.713
r_dihedral_angle_4_deg16.672
r_dihedral_angle_3_deg11.629
r_sphericity_free11.22
r_sphericity_bonded7.155
r_dihedral_angle_1_deg5.65
r_rigid_bond_restr2.127
r_angle_refined_deg1.36
r_angle_other_deg0.852
r_chiral_restr0.083
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms1688
Nucleic Acid Atoms
Solvent Atoms356
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SADABSdata scaling
PHASERphasing