5MAJ

CATHEPSIN L IN COMPLEX WITH 4-[cyclopentyl(imidazo[1,2-a]pyridin-2-ylmethyl)amino]-6-morpholino-1,3,5-triazine-2-carbonitrile


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529525% PEG3350, 0.2M ammonium acetate, 0.1M HEPES
Crystal Properties
Matthews coefficientSolvent content
2.0339.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.7α = 90
b = 57.061β = 90
c = 75.266γ = 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
1145.5196.10.034213.86.06102712
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)
111.0990.30.548525.4324065

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT145.5197604504096.120.138060.136390.16999RANDOM17.517
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]
0.21-0.650.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.57
r_sphericity_free25.026
r_dihedral_angle_4_deg15.497
r_sphericity_bonded13.88
r_dihedral_angle_3_deg13.129
r_rigid_bond_restr7.932
r_dihedral_angle_1_deg5.898
r_long_range_B_refined4.257
r_scbond_it3.465
r_mcangle_it2.809
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.57
r_sphericity_free25.026
r_dihedral_angle_4_deg15.497
r_sphericity_bonded13.88
r_dihedral_angle_3_deg13.129
r_rigid_bond_restr7.932
r_dihedral_angle_1_deg5.898
r_long_range_B_refined4.257
r_scbond_it3.465
r_mcangle_it2.809
r_angle_refined_deg2.449
r_mcbond_it2.103
r_chiral_restr0.157
r_bond_refined_d0.028
r_gen_planes_refined0.014
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 Atoms1688
Nucleic Acid Atoms
Solvent Atoms399
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
XPREPdata reduction
XSCALEdata scaling
PHASERphasing