2YJC

CATHEPSIN L WITH A NITRILE INHIBITOR


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1M MAGNESIUM FORMATE, 15 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.9537.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.997α = 90
b = 57.504β = 90
c = 75.708γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-03-17MSINGLE 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
11.145099.80.0513.146.2673833-317.63
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)
11.141.2499.60.492.325.81

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 DIFFRACTIONOTHERTHROUGHOUTNONE1.1445.7967306362795.970.147440.145460.18362RANDOM23.29
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]
-1.07-0.661.73
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free36.677
r_dihedral_angle_2_deg33.83
r_sphericity_bonded17.98
r_dihedral_angle_3_deg12.125
r_dihedral_angle_4_deg6.714
r_dihedral_angle_1_deg5.634
r_rigid_bond_restr2.573
r_angle_refined_deg1.431
r_angle_other_deg0.886
r_chiral_restr0.081
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free36.677
r_dihedral_angle_2_deg33.83
r_sphericity_bonded17.98
r_dihedral_angle_3_deg12.125
r_dihedral_angle_4_deg6.714
r_dihedral_angle_1_deg5.634
r_rigid_bond_restr2.573
r_angle_refined_deg1.431
r_angle_other_deg0.886
r_chiral_restr0.081
r_bond_other_d0.011
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_gen_planes_other0.003
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 Atoms287
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SADABSdata scaling
REFMACphasing