6QDC

Leishmania major N-myristoyltransferase in complex with thienopyrimidine inhibitor IMP-0000101


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4CGP 

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 = 47.672α = 90
b = 90.638β = 111.75
c = 53.113γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152012-09-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9790DiamondI04

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
11.44998.10.07411.64.780746
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)
11.41.42960.4882.23.8

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4CGP1.44976676404098.080.173060.171290.20761RANDOM17.607
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]
-0.290.140.29-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.997
r_dihedral_angle_4_deg17.715
r_dihedral_angle_3_deg15.727
r_dihedral_angle_1_deg6.33
r_long_range_B_refined5.293
r_scbond_it2.619
r_mcangle_it2.605
r_angle_refined_deg2.131
r_mcbond_it1.744
r_chiral_restr0.129
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.997
r_dihedral_angle_4_deg17.715
r_dihedral_angle_3_deg15.727
r_dihedral_angle_1_deg6.33
r_long_range_B_refined5.293
r_scbond_it2.619
r_mcangle_it2.605
r_angle_refined_deg2.131
r_mcbond_it1.744
r_chiral_restr0.129
r_bond_refined_d0.012
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 Atoms3354
Nucleic Acid Atoms
Solvent Atoms399
Heterogen Atoms114

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing