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Structures of the bacterial ribosome in classical and hybrid states of tRNA binding
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I1M PDB ENTRIES 3I1M, 3I1N, 3I1O, 3I1P experimental model PDB 3I1N PDB ENTRIES 3I1M, 3I1N, 3I1O, 3I1P experimental model PDB 3I1O PDB ENTRIES 3I1M, 3I1N, 3I1O, 3I1P experimental model PDB 3I1P PDB ENTRIES 3I1M, 3I1N, 3I1O, 3I1P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 291 PEG8000, MPD, pH 6.5, microbatch, temperature 291K 2 MICROBATCH 6.5 291 PEG8000, MPD, pH 6.5, microbatch, temperature 291K 3 MICROBATCH 6.5 291 PEG8000, MPD, pH 6.5, microbatch, temperature 291K 4 MICROBATCH 6.5 291 PEG8000, MPD, pH 6.5, microbatch, temperature 291K 5 MICROBATCH 6.5 291 PEG8000, MPD, pH 6.5, microbatch, temperature 291K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 211.67 α = 90 b = 438.07 β = 90 c = 613.42 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 2010-12-03 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2010-10-16 M SINGLE WAVELENGTH 3 1 x-ray 100 CCD ADSC QUANTUM 315 2010-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1 ALS 8.3.1 2 SYNCHROTRON ALS BEAMLINE 12.3.1 1.1 ALS 12.3.1 3 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97 APS 24-ID-C
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 1,2,3 3 40 83.5 0.194 7.38 938380 -3 51.273
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) 1,2,3 3 3.16 43.5 0.816 1.18
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS PDB ENTRIES 3I1M, 3I1N, 3I1O, 3I1P 3 40 1.8 938304 938304 19021 0.203 0.202 0.1937 0.26 0.248 RANDOM 41.6019
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19973 Nucleic Acid Atoms 34942 Solvent Atoms 203 Heterogen Atoms 72
Software Software Software Name Purpose XSCALE data processing PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection PHENIX model building XDS data reduction XDS data scaling PHENIX phasing