6GNU

Crystal Structure of Leishmania major N-Myristoyltransferase (NMT) With Bound Myristoyl-CoA and a Quionlinyl aryl sulphonamide ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H5Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.629126%PEG1500,0.2M NACL, 0.1M NACACODYLATE, PH 5.6
Crystal Properties
Matthews coefficientSolvent content
2.2144.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.309α = 90
b = 89.934β = 114.74
c = 52.884γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152011-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.93ESRFID14-4

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
11.544897.50.039213.459093
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)
11.541.5985.80.3642.92.9

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 REPLACEMENTTHROUGHOUT3h5z1.5444.9756088298597.430.15820.15670.1854RANDOM18.18
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]
0.08-0.01-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.429
r_dihedral_angle_4_deg20.53
r_dihedral_angle_3_deg15.469
r_dihedral_angle_1_deg6.891
r_angle_refined_deg2.403
r_angle_other_deg1.515
r_chiral_restr0.148
r_bond_refined_d0.025
r_gen_planes_refined0.012
r_gen_planes_other0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.429
r_dihedral_angle_4_deg20.53
r_dihedral_angle_3_deg15.469
r_dihedral_angle_1_deg6.891
r_angle_refined_deg2.403
r_angle_other_deg1.515
r_chiral_restr0.148
r_bond_refined_d0.025
r_gen_planes_refined0.012
r_gen_planes_other0.008
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3337
Nucleic Acid Atoms
Solvent Atoms270
Heterogen Atoms98

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing