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Structure-activity relationships at the 5-posiiton of thiolactomycin: an intact 5(R)-isoprene unit is required for activity against the condensing enzymes from Mycobacterium tuberculosis and Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FJ4 PDB ENTRY 1FJ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 290 1.9 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 2% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.6 51.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.118 α = 90 b = 138.997 β = 90 c = 212.458 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 170 CCD MARRESEARCH SI-220 2005-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97926 APS 22-ID
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 2.3 40 96.5 0.092 6 6.8 75836 75836 18
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) 2.3 2.4 87.2 0.152 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1FJ4 2.3 38.78 2 75836 71976 3800 96.15 0.18407 0.184 0.18173 0.2279 0.2115 RANDOM 18.219
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.992 r_dihedral_angle_4_deg 20.418 r_dihedral_angle_3_deg 16.287 r_dihedral_angle_1_deg 5.546 r_scangle_it 1.594 r_angle_refined_deg 1.138 r_scbond_it 0.997 r_angle_other_deg 0.783 r_mcangle_it 0.668 r_mcbond_it 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.992 r_dihedral_angle_4_deg 20.418 r_dihedral_angle_3_deg 16.287 r_dihedral_angle_1_deg 5.546 r_scangle_it 1.594 r_angle_refined_deg 1.138 r_scbond_it 0.997 r_angle_other_deg 0.783 r_mcangle_it 0.668 r_mcbond_it 0.61 r_symmetry_vdw_other 0.207 r_nbd_refined 0.192 r_nbd_other 0.183 r_symmetry_hbond_refined 0.172 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.132 r_symmetry_vdw_refined 0.119 r_nbtor_other 0.084 r_chiral_restr 0.067 r_mcbond_other 0.062 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11825 Nucleic Acid Atoms Solvent Atoms 538 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing