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Crystal Structure of Leishmania major N-myristoyltransferase (NMT) with bound myristoyl-CoA and a pyrazole sulphonamide ligand (DDD85646)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H5Z PDB ENTRY 3H5Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 25.9%PEG1500,0.2M NACL, 0.1M NACACODYLATE, PH 5.6
Crystal Properties Matthews coefficient Solvent content 2.22 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.51 α = 90 b = 90.317 β = 112.27 c = 52.972 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 CCD 2009-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.6 20 99.4 0.05 20.2 3.1 53906 17.4
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 1.6 1.66 99.9 0.51 2 3.2
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 PDB ENTRY 3H5Z 1.6 20 52161 1678 99.08 0.17714 0.176 0.1746 0.21296 0.2118 RANDOM 18.248
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] 1.1 0.44 -0.88 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.965 r_dihedral_angle_4_deg 18.652 r_dihedral_angle_3_deg 15.051 r_dihedral_angle_1_deg 6.207 r_scangle_it 3.89 r_scbond_it 2.591 r_angle_refined_deg 1.789 r_mcangle_it 1.629 r_mcbond_it 0.933 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.965 r_dihedral_angle_4_deg 18.652 r_dihedral_angle_3_deg 15.051 r_dihedral_angle_1_deg 6.207 r_scangle_it 3.89 r_scbond_it 2.591 r_angle_refined_deg 1.789 r_mcangle_it 1.629 r_mcbond_it 0.933 r_chiral_restr 0.115 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3346 Nucleic Acid Atoms Solvent Atoms 556 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing