9RLW | pdb_00009rlw

Leishmania major N-myristoyltransferase in complex with azetidinopyrimidine inhibitor IMP-825


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529130% PEG 1500, 0.2 M NaCl, 0.1 M Na cacodylate
Crystal Properties
Matthews coefficientSolvent content
2.2345

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.366α = 90
b = 91.721β = 112.923
c = 53.552γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2012-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.920DiamondI04-1

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
11.4949.498.90.03615.34.369322
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)
11.491.5299.60.8481.44.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUE1.4949.32369293343798.7830.1880.18550.18550.22690.226826.533
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]
0.007-0.6580.240.228
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.478
r_dihedral_angle_3_deg15.27
r_lrange_it7.199
r_dihedral_angle_1_deg6.656
r_scangle_it5.135
r_dihedral_angle_2_deg4.981
r_mcangle_it3.679
r_scbond_it3.495
r_mcbond_it2.574
r_angle_refined_deg2.257
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.478
r_dihedral_angle_3_deg15.27
r_lrange_it7.199
r_dihedral_angle_1_deg6.656
r_scangle_it5.135
r_dihedral_angle_2_deg4.981
r_mcangle_it3.679
r_scbond_it3.495
r_mcbond_it2.574
r_angle_refined_deg2.257
r_nbtor_refined0.316
r_symmetry_nbd_refined0.277
r_nbd_refined0.216
r_xyhbond_nbd_refined0.151
r_chiral_restr0.146
r_symmetry_xyhbond_nbd_refined0.129
r_bond_refined_d0.011
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3354
Nucleic Acid Atoms
Solvent Atoms389
Heterogen Atoms93

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing