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Crystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor IMP-0001114
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4B14
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 22% PEG 3350, 200 mM Ammonium Sulfate, 100 mM BisTris pH 5.5, 0.5mM IMP-0001114, 0.5mM myristoyl CoA: protein conc 12.53mg/mL: hdg0-1
Crystal Properties Matthews coefficient Solvent content 2.07 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.2 α = 90 b = 118.01 β = 90 c = 173.71 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 MARMOSAIC 300 mm CCD 2017-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
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 2.1 48.808 99.3 0.128 0.148 0.992 11.25 4.103 69068 -3 16.83
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 2.1 2.15 97 0.447 0.519 0.824 3.74 3.873
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4b14 2.1 48.808 1.35 69063 1977 99.3 0.1643 0.1626 0.1637 0.2212 0.2225 19.8306
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.868 f_angle_d 0.909 f_chiral_restr 0.055 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9311 Nucleic Acid Atoms Solvent Atoms 1002 Heterogen Atoms 388
Software Software Software Name Purpose XSCALE data scaling Coot model building PHENIX refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing