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Crystal structure of the peptolide 12C bound to bacterial ribosome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WDG 2WDG, 2WDH, 2WDI, 2WDJ experimental model PDB 2WDH 2WDG, 2WDH, 2WDI, 2WDJ experimental model PDB 2WDI 2WDG, 2WDH, 2WDI, 2WDJ experimental model PDB 2WDJ 2WDG, 2WDH, 2WDI, 2WDJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 3.5-4.5% PEG 20K, 3.5-4.5% PEG550 MME, 0.1M Tris-Acetate, 0.2M KSCN, 10 mM MgCl2 2 VAPOR DIFFUSION, SITTING DROP 7 293 3.5-4.5% PEG 20K, 3.5-4.5% PEG550 MME, 0.1M Tris-Acetate, 0.2M KSCN, 10 mM MgCl2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 209.24 α = 90 b = 443.46 β = 90 c = 618.62 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 315 2010-12-06 M SINGLE WAVELENGTH 2 1 100 CCD ADSC QUANTUM 315 2010-12-06 3 2 4 2
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9794 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.6 50 98 7.6 7.4 638335 91.29
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 3.6 3.7 95.8 1.169 1.8 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 MOLECULAR REPLACEMENT FREE R-VALUE 2WDG, 2WDH, 2WDI, 2WDJ 3.6 49.792 1.34 646099 29375 98.14 0.2237 0.2223 0.2245 0.2542 0.2539 79.9555
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.051 f_angle_d 0.887 f_chiral_restr 0.05 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 93223 Nucleic Acid Atoms 201478 Solvent Atoms Heterogen Atoms 786
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction HKL-2000 data reduction