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Crystal Structure of Leishmania major N-Myristoyltransferase (NMT) With Bound Myristoyl-CoA and a isopropyl methyl indole aryl sulphonamide ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H5Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 291 26% PEG1500, 0.2M NACL, 0.1M
NACACODYLATE, PH 5.6
Crystal Properties Matthews coefficient Solvent content 2.27 45.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.7 α = 90 b = 90.42 β = 114.83 c = 53.68 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 315 2011-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.98 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 48.7 99.4 0.091 10.4 3.4 21349
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 99.5 0.394 3.4 3.4
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 3h5z 2.2 45.21 19781 1548 99.29 0.1558 0.1516 0.1572 0.2077 0.2109 RANDOM 30.693
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] -0.18 -0.02 0.02 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.925 r_dihedral_angle_4_deg 20.906 r_dihedral_angle_3_deg 17.243 r_dihedral_angle_1_deg 6.841 r_angle_refined_deg 1.892 r_angle_other_deg 1.022 r_chiral_restr 0.108 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_gen_planes_other 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.925 r_dihedral_angle_4_deg 20.906 r_dihedral_angle_3_deg 17.243 r_dihedral_angle_1_deg 6.841 r_angle_refined_deg 1.892 r_angle_other_deg 1.022 r_chiral_restr 0.108 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_gen_planes_other 0.007 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3331 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing