5MAE

CATHEPSIN L IN COMPLEX WITH (2S,4R)-4-(2-Chloro-4-methoxy-benzenesulfonyl)-1-[3-(5-chloro-pyridin-2-yl)-azetidine-3-carbonyl]-pyrrolidine-2-car boxylic acid (1-cyano-cyclopropyl)-amide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherIn-house model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529525% PEG3350, 0.1M Bis-Tris
Crystal Properties
Matthews coefficientSolvent content
1.9737.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.529α = 90
b = 56.64β = 90
c = 73.916γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.0000SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
114599.60.043911.236.12103362
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)
111.0998.60.53072.065.4

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 model14598142513799.590.148940.147220.18213RANDOM16.088
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]
0.03-0.450.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.027
r_sphericity_free22.751
r_sphericity_bonded14.158
r_dihedral_angle_3_deg11.495
r_dihedral_angle_4_deg10.79
r_rigid_bond_restr8.51
r_dihedral_angle_1_deg5.92
r_long_range_B_refined4.038
r_scbond_it3.44
r_angle_refined_deg2.467
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.027
r_sphericity_free22.751
r_sphericity_bonded14.158
r_dihedral_angle_3_deg11.495
r_dihedral_angle_4_deg10.79
r_rigid_bond_restr8.51
r_dihedral_angle_1_deg5.92
r_long_range_B_refined4.038
r_scbond_it3.44
r_angle_refined_deg2.467
r_mcangle_it2.029
r_mcbond_it1.897
r_chiral_restr0.159
r_bond_refined_d0.03
r_gen_planes_refined0.017
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1674
Nucleic Acid Atoms
Solvent Atoms346
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
XPREPdata reduction
XSCALEdata scaling
PHASERphasing