6QDF

Leishmania major N-myristoyltransferase in complex with thienopyrimidine inhibitor IMP-0000096


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529130% PEG 1500, 0.2 M NACL, 0.1 M NA CACODYLATE, PH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.2345

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.519α = 90
b = 90.286β = 111.83
c = 53.01γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2012-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

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
11.494999.90.04611.53.467622
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)
11.491.5299.80.6411.53.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONAB INITIO PHASINGTHROUGHOUT1.494964224336599.840.174420.172460.2129RANDOM21.569
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]
0.33-0.090.06-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.4
r_dihedral_angle_4_deg20.339
r_dihedral_angle_3_deg15.113
r_dihedral_angle_1_deg6.761
r_long_range_B_refined5.8
r_scbond_it2.998
r_mcangle_it2.979
r_angle_refined_deg2.012
r_mcbond_it2
r_chiral_restr0.123
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.4
r_dihedral_angle_4_deg20.339
r_dihedral_angle_3_deg15.113
r_dihedral_angle_1_deg6.761
r_long_range_B_refined5.8
r_scbond_it2.998
r_mcangle_it2.979
r_angle_refined_deg2.012
r_mcbond_it2
r_chiral_restr0.123
r_bond_refined_d0.011
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_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 Atoms3354
Nucleic Acid Atoms
Solvent Atoms336
Heterogen Atoms91

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
REFMACphasing