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Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZJR PDB ENTRY 2ZJR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Crystal Properties Matthews coefficient Solvent content 4.46 72.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.59 α = 90 b = 410.204 β = 90 c = 695.078 γ = 90
Symmetry Space Group I 2 2 2
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 225 mm CCD MICROFOCUS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 3.2473 19.995 93.3 0.178 6.1 3.7 353603 0.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2473 3.36 34 1.2 2.2
Refinement Statistics Diffraction ID Structure Solution 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 ISOMORPHOUS REPLACEMENT PDB ENTRY 2ZJR 3.2473 19.995 0.61 353603 3564 93.3 0.253 0.252 0.2542 0.294 0.2952
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] -13.881 13.1054 -12.1603
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.927 f_angle_d 1.016 f_chiral_restr 0.075 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 24518 Nucleic Acid Atoms 59596 Solvent Atoms Heterogen Atoms 269
Software Software Software Name Purpose PHENIX model building PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling PHENIX phasing