5NTF

apo Structure of Leucyl aminopeptidase from Trypanosoma cruzi


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M Citric acid pH 4.0, 1.6 M (NH4)2SO4, 1 mM MnCl2, 5 mM actinonin
Crystal Properties
Matthews coefficientSolvent content
2.346.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 161.419α = 90
b = 161.419β = 90
c = 205.107γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
12.348.1496.20.1819.18.743976
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)
12.32.381000.9872.48.84437

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 REPLACEMENTTHROUGHOUT5NTG2.348.1441496206195.290.211520.209220.25906RANDOM30.635
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]
-1.78-0.89-1.785.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.181
r_dihedral_angle_3_deg14.282
r_dihedral_angle_4_deg12.847
r_dihedral_angle_1_deg6.326
r_long_range_B_refined4.812
r_long_range_B_other4.807
r_scangle_other3.218
r_mcangle_it2.661
r_mcangle_other2.661
r_scbond_it1.973
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.181
r_dihedral_angle_3_deg14.282
r_dihedral_angle_4_deg12.847
r_dihedral_angle_1_deg6.326
r_long_range_B_refined4.812
r_long_range_B_other4.807
r_scangle_other3.218
r_mcangle_it2.661
r_mcangle_other2.661
r_scbond_it1.973
r_scbond_other1.973
r_mcbond_it1.637
r_mcbond_other1.636
r_angle_refined_deg1.402
r_angle_other_deg1.211
r_chiral_restr0.078
r_bond_refined_d0.012
r_bond_other_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.004
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 Atoms7523
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing