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Crystal structure of the E. coli ribosome bound to negamycin.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 291 PEG8k, MPD
Crystal Properties Matthews coefficient Solvent content 3.38 63.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 211.91 α = 90 b = 434.31 β = 90 c = 624.4 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 PIXEL DECTRIS PILATUS 6M 2014-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 3.09 41.14 99.9 0.13 0.058 0.994 14.9 5.9 1043787 72.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.09 3.27 100 0.804 0.358 0.749 2.6 6 168100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 3.09 41.136 1.89 1039051 4190 99.94 0.2019 0.2018 0.2038 0.2444 0.2461 67.48
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 16.354 f_angle_d 1.252 f_chiral_restr 0.053 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 90489 Nucleic Acid Atoms 195478 Solvent Atoms 203 Heterogen Atoms 72
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction