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Crystal structure of Aspergillus fumigatus N-myristoyl transferase in complex with myristoyl CoA and a dimethylpyridyl-dipihenyl-pyridine ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CAX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 25%PEG3350,0.2M NACL
Crystal Properties Matthews coefficient Solvent content 2.51 51.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.432 α = 90 b = 58.895 β = 90 c = 152.787 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 ADSC QUANTUM 4 2009-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.933 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 1.8 50 94.5 0.041 30 2.8 40875
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 1.8 1.86 95.7 0.138 7.5 2.7
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 4CAX 1.8 19.82 38780 2043 94.48 0.17525 0.17332 0.1823 0.21254 0.2234 RANDOM 19.892
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] 0.04 0.04 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.008 r_dihedral_angle_4_deg 18.132 r_dihedral_angle_3_deg 13.059 r_dihedral_angle_1_deg 6.332 r_long_range_B_refined 6.01 r_long_range_B_other 5.902 r_scangle_other 4.298 r_scbond_it 2.994 r_scbond_other 2.994 r_mcangle_it 2.621
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.008 r_dihedral_angle_4_deg 18.132 r_dihedral_angle_3_deg 13.059 r_dihedral_angle_1_deg 6.332 r_long_range_B_refined 6.01 r_long_range_B_other 5.902 r_scangle_other 4.298 r_scbond_it 2.994 r_scbond_other 2.994 r_mcangle_it 2.621 r_mcangle_other 2.621 r_angle_other_deg 2.246 r_mcbond_it 1.945 r_mcbond_other 1.944 r_angle_refined_deg 1.471 r_chiral_restr 0.092 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_gen_planes_other 0.008 r_bond_other_d 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 3184 Nucleic Acid Atoms Solvent Atoms 514 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing