6QD9

Leishmania major N-myristoyltransferase in complex with thienopyrimidine inhibitor IMP-0000065


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 = 47.72α = 90
b = 90.78β = 111.92
c = 53.03γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152012-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.464597.70.05414.34.1709132
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)
11.461.587.90.512.13.7

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 SYNTHESISTHROUGHOUT4CGP1.4637.7467332358097.690.168020.16630.20017RANDOM14.808
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]
0.04-0.260.31-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.353
r_dihedral_angle_4_deg19.376
r_dihedral_angle_3_deg14.181
r_dihedral_angle_1_deg6.42
r_long_range_B_refined4.861
r_scbond_it2.216
r_mcangle_it2.076
r_angle_refined_deg2.031
r_mcbond_it1.355
r_chiral_restr0.123
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.353
r_dihedral_angle_4_deg19.376
r_dihedral_angle_3_deg14.181
r_dihedral_angle_1_deg6.42
r_long_range_B_refined4.861
r_scbond_it2.216
r_mcangle_it2.076
r_angle_refined_deg2.031
r_mcbond_it1.355
r_chiral_restr0.123
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 Atoms575
Heterogen Atoms87

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing