5NSQ

Structure of Leucyl aminopeptidase from Trypanosoma brucei 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 DROP2930.1 M Tris pH 8.0, 2.4 M (NH4)2SO4, 5 mM MnSO4, 5 mM actinonin
Crystal Properties
Matthews coefficientSolvent content
2.6954.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.909α = 90
b = 165.73β = 112.45
c = 121.98γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2013-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9200DiamondI04-1

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
1341.5970.1164.53.268219
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)
133.07980.4423.24424

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 REPLACEMENTTHROUGHOUT5NSK341.563948332795.520.266170.264640.29641RANDOM35.895
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]
1.080.22-3.671.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.439
r_dihedral_angle_3_deg14.316
r_dihedral_angle_4_deg12.986
r_long_range_B_refined6.16
r_long_range_B_other6.16
r_dihedral_angle_1_deg6.039
r_mcangle_it4.593
r_mcangle_other4.593
r_scangle_other3.632
r_mcbond_it2.773
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.439
r_dihedral_angle_3_deg14.316
r_dihedral_angle_4_deg12.986
r_long_range_B_refined6.16
r_long_range_B_other6.16
r_dihedral_angle_1_deg6.039
r_mcangle_it4.593
r_mcangle_other4.593
r_scangle_other3.632
r_mcbond_it2.773
r_mcbond_other2.772
r_scbond_it2.087
r_scbond_other2.087
r_angle_refined_deg1.443
r_angle_other_deg1.254
r_chiral_restr0.072
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.006
r_gen_planes_other0.005
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 Atoms22467
Nucleic Acid Atoms
Solvent Atoms34
Heterogen Atoms174

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing