5MQY

CATHEPSIN L IN COMPLEX WITH 4-[1,3-benzodioxol-5-ylmethyl(2-phenoxyethyl)amino]-5-fluoropyrimidine-2-carbonitrile


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5F02 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529425% PEG3350, 0.1M Bis-Tris
Crystal Properties
Matthews coefficientSolvent content
2.0640.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.907α = 90
b = 57.2β = 90
c = 75.735γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-08-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.0000SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.1339.2699.80.04280.042813.656.1575222
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)
11.131.2399.70.7851.045.75

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 REPLACEMENTTHROUGHOUT5F021.1339.2671261371299.530.151050.148690.19898RANDOM23.934
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]
-0.160.23-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.794
r_sphericity_free30.698
r_dihedral_angle_4_deg20.933
r_sphericity_bonded18.394
r_dihedral_angle_3_deg11.68
r_rigid_bond_restr8.697
r_dihedral_angle_1_deg5.897
r_long_range_B_refined4.777
r_scbond_it4.023
r_mcangle_it3.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.794
r_sphericity_free30.698
r_dihedral_angle_4_deg20.933
r_sphericity_bonded18.394
r_dihedral_angle_3_deg11.68
r_rigid_bond_restr8.697
r_dihedral_angle_1_deg5.897
r_long_range_B_refined4.777
r_scbond_it4.023
r_mcangle_it3.34
r_mcbond_it2.966
r_angle_refined_deg2.792
r_chiral_restr0.197
r_bond_refined_d0.032
r_gen_planes_refined0.018
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 Atoms1666
Nucleic Acid Atoms
Solvent Atoms251
Heterogen Atoms61

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PHASERphasing