6GNH

Crystal Structure of Leishmania major N-Myristoyltransferase (NMT) With Bound Myristoyl-CoA and an Azepanyl Phenyl Benzylsulphonamide Ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WSA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.629126%PEG1500,0.2M NACL, 0.1M NACACODYLATE, PH 5.6
Crystal Properties
Matthews coefficientSolvent content
2.2745.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.613α = 90
b = 90.99β = 114.61
c = 53.561γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102009-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.933ESRFID14-1

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
11.8950860.06715328979
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.891.9652.4

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 REPLACEMENTTHROUGHOUT2WSA1.8938.7127527143785.910.17180.16850.2334RANDOM19.419
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]
0.04-0.03-0.020.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.072
r_dihedral_angle_4_deg21.361
r_dihedral_angle_3_deg16.28
r_dihedral_angle_1_deg6.992
r_angle_other_deg1.985
r_angle_refined_deg1.931
r_chiral_restr0.125
r_bond_refined_d0.019
r_gen_planes_other0.015
r_gen_planes_refined0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.072
r_dihedral_angle_4_deg21.361
r_dihedral_angle_3_deg16.28
r_dihedral_angle_1_deg6.992
r_angle_other_deg1.985
r_angle_refined_deg1.931
r_chiral_restr0.125
r_bond_refined_d0.019
r_gen_planes_other0.015
r_gen_planes_refined0.009
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3339
Nucleic Acid Atoms
Solvent Atoms383
Heterogen Atoms92

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing