2YJB

CATHEPSIN L WITH A NITRILE INHIBITOR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YJ2PDB ENTRY 2YJ2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.1 M BIS-TRIS PH 6.5, 0.2 M NACL, 25% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.7529.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.365α = 90
b = 58.495β = 90
c = 64.042γ = 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
11.45095.50.18.915.9933489-318.66
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)
11.41.591.60.661.655.42

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 2YJ21.446.3730210160490.890.161810.158870.21779RANDOM18.053
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]
-0.51-1.892.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.197
r_sphericity_free28.222
r_dihedral_angle_4_deg13.827
r_dihedral_angle_3_deg11.716
r_sphericity_bonded8.548
r_dihedral_angle_1_deg5.827
r_rigid_bond_restr2.685
r_angle_refined_deg1.363
r_angle_other_deg0.886
r_chiral_restr0.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.197
r_sphericity_free28.222
r_dihedral_angle_4_deg13.827
r_dihedral_angle_3_deg11.716
r_sphericity_bonded8.548
r_dihedral_angle_1_deg5.827
r_rigid_bond_restr2.685
r_angle_refined_deg1.363
r_angle_other_deg0.886
r_chiral_restr0.087
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 Atoms1697
Nucleic Acid Atoms
Solvent Atoms231
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SADABSdata scaling
PHASERphasing