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Crystal Structure of a 70S Ribosome-tRNA Complex Reveals Functional Interactions and Rearrangements.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model ModelArchive ma-ce688 entries 1TWT AND 1TWV that were moved from PDB to ModelArchive in silico model ModelArchive ma-cbwe8 entries 1TWT AND 1TWV that were moved from PDB to ModelArchive
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 24-26% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 5 75.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 507.81 α = 90 b = 507.81 β = 90 c = 689.52 γ = 90
Symmetry Space Group I 4 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 ADSC QUANTUM 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 ALS 12.3.1
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 3.7 75 99.3 0.149 5.4 465894 1.5
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 3.7 3.8 96.6 0.467 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entries 1TWT AND 1TWV 3.71 30 455685 11345 100 0.349 0.349 0.348 0.3339 0.353 0.3401 RANDOM
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 r_dihedral_angle_2_deg 41.009 r_mcangle_it 35.427 r_mcbond_it 25.357 r_dihedral_angle_3_deg 17.715 r_dihedral_angle_4_deg 16.421 r_scangle_it 10.125 r_scbond_it 5.208 r_dihedral_angle_1_deg 2.795 r_angle_refined_deg 1.393 r_symmetry_vdw_refined 0.488
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.009 r_mcangle_it 35.427 r_mcbond_it 25.357 r_dihedral_angle_3_deg 17.715 r_dihedral_angle_4_deg 16.421 r_scangle_it 10.125 r_scbond_it 5.208 r_dihedral_angle_1_deg 2.795 r_angle_refined_deg 1.393 r_symmetry_vdw_refined 0.488 r_nbd_refined 0.417 r_symmetry_hbond_refined 0.366 r_xyhbond_nbd_refined 0.326 r_nbtor_refined 0.322 r_chiral_restr 0.109 r_gen_planes_refined 0.015 r_bond_refined_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26862 Nucleic Acid Atoms 64786 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection CNS refinement d*TREK data reduction CCP4 data scaling CNS phasing