5NSK

apo Structure of Leucyl aminopeptidase from Trypanosoma brucei


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HB62HB6 poly-Ala model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.8 M Na citrate pH 7.0, 5 mM CoSO4
Crystal Properties
Matthews coefficientSolvent content
3.5164.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 162.33α = 90
b = 162.45β = 90
c = 176.99γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-04-27MSINGLE 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
12.672.611000.1659.57.4143992
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)
12.62.641001.01927.57106

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 REPLACEMENTTHROUGHOUT2HB6 poly-Ala model2.672.61136637725799.990.192120.191130.21085RANDOM38.096
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]
-1.810.711.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.344
r_dihedral_angle_4_deg20.352
r_dihedral_angle_3_deg13.692
r_dihedral_angle_1_deg6.017
r_long_range_B_refined5.181
r_long_range_B_other5.169
r_scangle_other3.593
r_mcangle_it3.377
r_mcangle_other3.377
r_scbond_it2.257
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.344
r_dihedral_angle_4_deg20.352
r_dihedral_angle_3_deg13.692
r_dihedral_angle_1_deg6.017
r_long_range_B_refined5.181
r_long_range_B_other5.169
r_scangle_other3.593
r_mcangle_it3.377
r_mcangle_other3.377
r_scbond_it2.257
r_scbond_other2.257
r_mcbond_it2.076
r_mcbond_other2.076
r_angle_other_deg2.006
r_angle_refined_deg1.532
r_chiral_restr0.085
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.008
r_gen_planes_other0.007
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 Atoms22152
Nucleic Acid Atoms
Solvent Atoms500
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing