4QBJ

Crystal structure of N-myristoyl transferase from Aspergillus fumigatus complexed with a synthetic inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IIC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2981.85-2.3M ammonium sulfate, 0.1M HEPES, 20mM MnCl2, 1mM TCEP, pH 7.1-7.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6152.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.792α = 90
b = 77.074β = 90
c = 113.237γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayIMAGE PLATERIGAKU RAXIS IIC2003-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.542

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.110028569

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 REPLACEMENTTHROUGHOUT1IIC2.12527147142199.590.178650.176690.21745RANDOM36.839
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]
0.560.02-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.487
r_dihedral_angle_4_deg18.75
r_dihedral_angle_3_deg15.028
r_long_range_B_refined9.699
r_dihedral_angle_1_deg6.188
r_scbond_it5.706
r_mcangle_it4.968
r_mcbond_it3.63
r_angle_refined_deg2.081
r_chiral_restr0.141
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.487
r_dihedral_angle_4_deg18.75
r_dihedral_angle_3_deg15.028
r_long_range_B_refined9.699
r_dihedral_angle_1_deg6.188
r_scbond_it5.706
r_mcangle_it4.968
r_mcbond_it3.63
r_angle_refined_deg2.081
r_chiral_restr0.141
r_bond_refined_d0.018
r_gen_planes_refined0.012
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_it
r_scangle_other
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 Atoms3140
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms112

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling