5T6H

Crystal structure of Aspergillus fumigatus N-myristoyl transferase in complex with myristoyl CoA and a dimethylpyridyl-dipihenyl-pyridine 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
2.5151.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.432α = 90
b = 58.895β = 90
c = 152.787γ = 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)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
11.85094.50.041302.840875
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)
11.81.8695.70.1387.52.7

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 REPLACEMENTTHROUGHOUT4CAX1.819.8238780204394.480.175250.173320.21254RANDOM19.892
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]
0.040.04-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.008
r_dihedral_angle_4_deg18.132
r_dihedral_angle_3_deg13.059
r_dihedral_angle_1_deg6.332
r_long_range_B_refined6.01
r_long_range_B_other5.902
r_scangle_other4.298
r_scbond_it2.994
r_scbond_other2.994
r_mcangle_it2.621
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.008
r_dihedral_angle_4_deg18.132
r_dihedral_angle_3_deg13.059
r_dihedral_angle_1_deg6.332
r_long_range_B_refined6.01
r_long_range_B_other5.902
r_scangle_other4.298
r_scbond_it2.994
r_scbond_other2.994
r_mcangle_it2.621
r_mcangle_other2.621
r_angle_other_deg2.246
r_mcbond_it1.945
r_mcbond_other1.944
r_angle_refined_deg1.471
r_chiral_restr0.092
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_gen_planes_other0.008
r_bond_other_d0.001
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 Atoms3184
Nucleic Acid Atoms
Solvent Atoms514
Heterogen Atoms93

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing