5T6E

Crystal structure of Aspergillus fumigatus N-myristoyl transferase in complex with myristoyl CoA and a dichloro-dimethylpyridyl-methoxy-phenyl-pyridyl-piperazine ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4CAX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29125%PEG3350,0.2M NACL
Crystal Properties
Matthews coefficientSolvent content
2.5251.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.276α = 90
b = 58.339β = 90
c = 152.1γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42009-04-30MSINGLE 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)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
12.348.5999.40.0880.9969.23.82081932
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.391000.4780.7621.93.8

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 REPLACEMENTTHROUGHOUT4CAX2.348.519736107098.970.198990.196280.24788RANDOM40.343
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]
-3.44-0.213.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.811
r_dihedral_angle_4_deg19.094
r_dihedral_angle_3_deg15.125
r_dihedral_angle_1_deg6.503
r_long_range_B_refined5.96
r_long_range_B_other5.952
r_scangle_other4.255
r_mcangle_it3.511
r_mcangle_other3.51
r_scbond_it2.821
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.811
r_dihedral_angle_4_deg19.094
r_dihedral_angle_3_deg15.125
r_dihedral_angle_1_deg6.503
r_long_range_B_refined5.96
r_long_range_B_other5.952
r_scangle_other4.255
r_mcangle_it3.511
r_mcangle_other3.51
r_scbond_it2.821
r_scbond_other2.821
r_mcbond_it2.352
r_mcbond_other2.352
r_angle_refined_deg1.395
r_angle_other_deg0.795
r_chiral_restr0.074
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3188
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms93

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing