6NXG

Crystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor 303a


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293PlviB.18219.a.FR2.PS38192 at 13.5 mg/mL was incubated with final concentrations of 0.8 mM Myristoyl-CoA and 0.8 mM compound at 4C for 30 min, then mixed with 1:1 with 0.06M Magnesium chloride hexahydrate: 0.0.06M Calcium chloride dihydrate, 0.1M Tris (base): BICINE 49 % of Precipitant Mix 1 (40% (v/v) PEG 500-MME: 20 % (w/v) PEG 20000
Crystal Properties
Matthews coefficientSolvent content
2.1141.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.42α = 90
b = 119.03β = 90
c = 175.35γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002016-11-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97857APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
11.649.291000.0880.0960.99814.826.315887818.869
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.641000.5390.5890.8733.26.2

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 REPLACEMENTTHROUGHOUT2ynd1.649.29150955792399.960.150370.149110.17409RANDOM12.489
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]
-0.54-0.040.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.689
r_dihedral_angle_4_deg16.456
r_dihedral_angle_3_deg13.178
r_dihedral_angle_1_deg6.916
r_long_range_B_refined4.712
r_long_range_B_other4.712
r_angle_refined_deg1.426
r_angle_other_deg1.368
r_scangle_other1.234
r_mcangle_it1.069
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.689
r_dihedral_angle_4_deg16.456
r_dihedral_angle_3_deg13.178
r_dihedral_angle_1_deg6.916
r_long_range_B_refined4.712
r_long_range_B_other4.712
r_angle_refined_deg1.426
r_angle_other_deg1.368
r_scangle_other1.234
r_mcangle_it1.069
r_mcangle_other1.069
r_scbond_it0.766
r_scbond_other0.766
r_mcbond_it0.601
r_mcbond_other0.601
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9463
Nucleic Acid Atoms
Solvent Atoms1687
Heterogen Atoms277

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing