8FI5

Crystal Structure of Glycylpeptide N-tetradecanoyltransferase (N-myristoyl transferase) (NMT) from Leishmania major Friedlin bound to tetradecanoyl-CoA (Orthorhombic P Form 2)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6OMK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP92910.1 M Bicine, 20% PEG 6000, LemaA.18219.a.B2.PS38707 at 11.17 mg/mL. Tray: Tray 383B3/1 mM Perez-1, Puck: HR00406_03, Cryo: 20% PEG ethylene glycol. MYA ligand was acquired from the expression host and not added prior to crystallization.
Crystal Properties
Matthews coefficientSolvent content
2.5351.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.499α = 90
b = 90.238β = 90
c = 92.523γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2022-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 19-ID0.9786NSLS-II19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.2549.671000.1050.1120.0370.998129.124336
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.321001.2251.3030.4380.7158.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.2549.671.1124260120299.870.18910.18610.2422
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_d14.246
f_angle_d1.14
f_chiral_restr0.06
f_bond_d0.012
f_plane_restr0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3294
Nucleic Acid Atoms
Solvent Atoms96
Heterogen Atoms63

Software

Software
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing