5NDK
Crystal structure of aminoglycoside TC007 co-crystallized with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA
This is a non-PDB format compatible entry.
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SLS BEAMLINE X06SA |
| Synchrotron site | SLS |
| Beamline | X06SA |
| Temperature [K] | 90 |
| Detector technology | PIXEL |
| Collection date | 2016-05-25 |
| Detector | DECTRIS EIGER X 16M |
| Wavelength(s) | 1.0 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 209.070, 447.360, 619.490 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 152.739 - 2.950 |
| R-factor | 0.2135 |
| Rwork | 0.213 |
| R-free | 0.25310 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.013 |
| RMSD bond angle | 1.915 |
| Data reduction software | XDS |
| Data scaling software | XSCALE |
| Phasing software | PHENIX |
| Refinement software | PHENIX |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 152.739 | 300.000 | 3.050 |
| High resolution limit [Å] | 2.950 | 200.000 | 2.950 |
| Rmerge | 0.307 | 2.574 | |
| Rmeas | 0.310 | 2.636 | |
| Total number of observations | 56386821 | ||
| Number of reflections | 1204009 | 113823 | |
| <I/σ(I)> | 16.04 | 1.38 | |
| Completeness [%] | 100.0 | 100 | |
| Redundancy | 46.833 | 21.11 | |
| CC(1/2) | 0.994 | 0.471 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 4% PEG20K, 4% PEGMME 550, 100mM Tris/HAc, 200mM KSCN |
