5NTG

Structure of Leucyl aminopeptidase from Trypanosoma cruzi in complex with citrate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M Phosphate-citrate pH 4.2, 40 % (v/v) PEG 300, 5 mM MnSO4, 5 mM amastatin
Crystal Properties
Matthews coefficientSolvent content
2.2445.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 160.12α = 90
b = 160.12β = 90
c = 203.672γ = 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
12.3257.311000.188111143546
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)
12.322.41001.20211.1

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 REPLACEMENTTHROUGHOUT5NSK2.3257.3141361218399.980.167720.165520.20997RANDOM31.21
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]
-1.73-0.86-1.735.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.266
r_dihedral_angle_3_deg14.892
r_dihedral_angle_4_deg13.011
r_dihedral_angle_1_deg6.527
r_long_range_B_other5.661
r_long_range_B_refined5.66
r_scangle_other4.036
r_mcangle_it2.768
r_mcangle_other2.767
r_scbond_it2.551
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.266
r_dihedral_angle_3_deg14.892
r_dihedral_angle_4_deg13.011
r_dihedral_angle_1_deg6.527
r_long_range_B_other5.661
r_long_range_B_refined5.66
r_scangle_other4.036
r_mcangle_it2.768
r_mcangle_other2.767
r_scbond_it2.551
r_scbond_other2.535
r_mcbond_it1.741
r_mcbond_other1.74
r_angle_refined_deg1.544
r_angle_other_deg1.258
r_chiral_restr0.109
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.006
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 Atoms7610
Nucleic Acid Atoms
Solvent Atoms382
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing