5NTH

Structure of Leucyl aminopeptidase from Leishmania major in complex with actinonin


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.8 M Succinic acid pH 7.0, 3 % (w/v) 1,5-Diamino-pentane di-hydrochloride, 5 mM MnSO4, 5 mM actinonin
Crystal Properties
Matthews coefficientSolvent content
3.1360.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.439α = 90
b = 116.439β = 90
c = 91.491γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.97781DiamondI24

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
12.538.1187.80.158.25.721850
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)
12.52.690.20.74725.6

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 REPLACEMENTTHROUGHOUT5NSK2.538.1120818103186.720.196490.193970.24486RANDOM32.765
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]
-1.71-0.85-1.715.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.313
r_dihedral_angle_4_deg17.932
r_dihedral_angle_3_deg16.235
r_dihedral_angle_1_deg6.993
r_long_range_B_refined4.187
r_long_range_B_other4.187
r_scangle_other2.614
r_mcangle_it2.474
r_mcangle_other2.473
r_scbond_it1.726
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.313
r_dihedral_angle_4_deg17.932
r_dihedral_angle_3_deg16.235
r_dihedral_angle_1_deg6.993
r_long_range_B_refined4.187
r_long_range_B_other4.187
r_scangle_other2.614
r_mcangle_it2.474
r_mcangle_other2.473
r_scbond_it1.726
r_scbond_other1.726
r_angle_refined_deg1.642
r_mcbond_it1.459
r_mcbond_other1.456
r_angle_other_deg1
r_chiral_restr0.083
r_bond_refined_d0.013
r_bond_other_d0.006
r_gen_planes_refined0.006
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3893
Nucleic Acid Atoms
Solvent Atoms49
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing