7A0R
50S Deinococcus radiodurans ribosome bounded with mycinamicin I
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ESRF BEAMLINE ID23-2 |
Synchrotron site | ESRF |
Beamline | ID23-2 |
Temperature [K] | 80 |
Detector technology | PIXEL |
Collection date | 2016-02-02 |
Detector | DECTRIS PILATUS3 2M |
Wavelength(s) | 0.873 |
Spacegroup name | I 2 2 2 |
Unit cell lengths | 170.484, 408.933, 697.322 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 49.545 - 3.300 |
R-factor | 0.2168 |
Rwork | 0.215 |
R-free | 0.24920 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3pio |
RMSD bond length | 0.008 |
RMSD bond angle | 1.378 |
Data reduction software | HKL-2000 |
Data scaling software | HKL-2000 |
Phasing software | PHENIX (1.12_2829) |
Refinement software | PHENIX (1.12_2829) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 3.360 |
High resolution limit [Å] | 3.300 | 8.940 | 3.300 |
Rmerge | 0.182 | 0.119 | 1.145 |
Rmeas | 0.215 | 0.142 | 1.355 |
Rpim | 0.113 | 0.076 | 0.711 |
Total number of observations | 1224927 | ||
Number of reflections | 359719 | 18190 | 17979 |
<I/σ(I)> | 5.5 | ||
Completeness [%] | 98.4 | 95.8 | 99 |
Redundancy | 3.4 | 3.4 | 3.3 |
CC(1/2) | 0.960 | 0.550 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 293.15 | Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir. |