4CAV

Crystal structure of Aspergillus fumigatus N-myristoyl transferase in complex with myristoyl CoA and a benzofuran ligand R0-09-4879


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IYKPDB ENTRY 1IYK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.525% PEG3350, 0.2M NACL, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.5151

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.43α = 90
b = 57.011β = 90
c = 143.388γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2008-10-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM16ESRFBM16

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
11.92595.10.07273.2333892
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)
11.91.9791.80.284.63.1

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 1IYK1.8919.9333387176694.110.18890.185790.24835RANDOM24.788
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]
-0.020.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.495
r_dihedral_angle_4_deg19.182
r_dihedral_angle_3_deg16.046
r_dihedral_angle_1_deg7.085
r_scangle_it4.839
r_scbond_it3.256
r_angle_refined_deg2.18
r_mcangle_it1.917
r_mcbond_it1.172
r_chiral_restr0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.495
r_dihedral_angle_4_deg19.182
r_dihedral_angle_3_deg16.046
r_dihedral_angle_1_deg7.085
r_scangle_it4.839
r_scbond_it3.256
r_angle_refined_deg2.18
r_mcangle_it1.917
r_mcbond_it1.172
r_chiral_restr0.17
r_bond_refined_d0.023
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 Atoms3188
Nucleic Acid Atoms
Solvent Atoms412
Heterogen Atoms97

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing