2WSA

Crystal Structure of Leishmania major N-myristoyltransferase (NMT) with bound myristoyl-CoA and a pyrazole sulphonamide ligand (DDD85646)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H5ZPDB ENTRY 3H5Z

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.525.9%PEG1500,0.2M NACL, 0.1M NACACODYLATE, PH 5.6
Crystal Properties
Matthews coefficientSolvent content
2.2244

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.51α = 90
b = 90.317β = 112.27
c = 52.972γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2009-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.62099.40.0520.23.15390617.4
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)
11.61.6699.90.5123.2

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3H5Z1.62052161167899.080.177140.1760.21296RANDOM18.248
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]
1.10.44-0.880.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.965
r_dihedral_angle_4_deg18.652
r_dihedral_angle_3_deg15.051
r_dihedral_angle_1_deg6.207
r_scangle_it3.89
r_scbond_it2.591
r_angle_refined_deg1.789
r_mcangle_it1.629
r_mcbond_it0.933
r_chiral_restr0.115
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.965
r_dihedral_angle_4_deg18.652
r_dihedral_angle_3_deg15.051
r_dihedral_angle_1_deg6.207
r_scangle_it3.89
r_scbond_it2.591
r_angle_refined_deg1.789
r_mcangle_it1.629
r_mcbond_it0.933
r_chiral_restr0.115
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3346
Nucleic Acid Atoms
Solvent Atoms556
Heterogen Atoms95

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing