5T5U

Crystal structure of Aspergillus fumigatus N-myristoyl transferase in complex with myristoyl CoA and a methylpyridyl-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
2.5251.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.035α = 90
b = 58.403β = 90
c = 152.635γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4r2009-02-02MSINGLE 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
11.842.4990.0510.99712.92.84241213.5
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)
11.81.8496.20.2620.8523.42.8

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 REPLACEMENTTHROUGHOUT4CAX1.842.440240214498.450.210430.208920.23821RANDOM18.201
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]
-0.74-0.120.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.59
r_dihedral_angle_4_deg15.97
r_dihedral_angle_3_deg13.306
r_dihedral_angle_1_deg5.892
r_long_range_B_refined4.802
r_long_range_B_other4.66
r_scangle_other3.524
r_scbond_it2.543
r_scbond_other2.542
r_mcangle_it2.433
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.59
r_dihedral_angle_4_deg15.97
r_dihedral_angle_3_deg13.306
r_dihedral_angle_1_deg5.892
r_long_range_B_refined4.802
r_long_range_B_other4.66
r_scangle_other3.524
r_scbond_it2.543
r_scbond_other2.542
r_mcangle_it2.433
r_mcangle_other2.433
r_angle_other_deg1.814
r_mcbond_it1.805
r_mcbond_other1.804
r_angle_refined_deg1.187
r_chiral_restr0.067
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_gen_planes_other0.004
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 Atoms3185
Nucleic Acid Atoms
Solvent Atoms437
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing