4R76

Structure of the m17 leucyl aminopeptidase from malaria complexed with a hydroxamic acid-based inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KQZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.529840% (v/v) PEG 400, 0.1 M Tris pH 8.5, 0.2 M Li2SO4, 1 mM TCEP, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5451.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 174.041α = 90
b = 177.408β = 90
c = 231.77γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.95370Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.146.597.221099723.39

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT3KQZ2.536.212106751041185.40.2090.2070.24828.72
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.062
f_angle_d0.65
f_chiral_restr0.026
f_bond_d0.003
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms46790
Nucleic Acid Atoms
Solvent Atoms1796
Heterogen Atoms568

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
GDAdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing