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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 4.4 72.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.723 α = 90 b = 408.562 β = 90 c = 693.334 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 PIXEL PSI PILATUS 6M M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3.45 19.998 84.3 0.216 0.096 5.6 4.6 260194 0.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.45 3.57 85.6 1.4 4.5
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 3.45 19.998 0.58 260194 2635 83.3 0.257 0.257 0.2609 0.301 0.2996
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] -20.514 6.816 -25.6717
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.358 f_angle_d 1.271 f_chiral_restr 0.067 f_bond_d 0.013 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 24479 Nucleic Acid Atoms 59311 Solvent Atoms Heterogen Atoms 173
Software Software Software Name Purpose PHENIX model building PHENIX refinement MOSFLM data reduction SCALA data scaling PHENIX phasing