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Crystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor 303a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YND
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 PlviB.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 coefficient Solvent content 2.11 41.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.42 α = 90 b = 119.03 β = 90 c = 175.35 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 2016-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.6 49.29 100 0.088 0.096 0.998 14.82 6.3 158878 18.869
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) Redundancy Number Unique Reflections (All) 1 1.6 1.64 100 0.539 0.589 0.873 3.2 6.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2ynd 1.6 49.29 150955 7923 99.96 0.15037 0.14911 0.1634 0.17409 0.186 RANDOM 12.489
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 -0.04 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.689 r_dihedral_angle_4_deg 16.456 r_dihedral_angle_3_deg 13.178 r_dihedral_angle_1_deg 6.916 r_long_range_B_refined 4.712 r_long_range_B_other 4.712 r_angle_refined_deg 1.426 r_angle_other_deg 1.368 r_scangle_other 1.234 r_mcangle_it 1.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.689 r_dihedral_angle_4_deg 16.456 r_dihedral_angle_3_deg 13.178 r_dihedral_angle_1_deg 6.916 r_long_range_B_refined 4.712 r_long_range_B_other 4.712 r_angle_refined_deg 1.426 r_angle_other_deg 1.368 r_scangle_other 1.234 r_mcangle_it 1.069 r_mcangle_other 1.069 r_scbond_it 0.766 r_scbond_other 0.766 r_mcbond_it 0.601 r_mcbond_other 0.601 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 9463 Nucleic Acid Atoms Solvent Atoms 1687 Heterogen Atoms 277
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing