6HHY
Klebsiella pneumoniae Seryl-tRNA Synthetase in Complex with 5'-O-(N-(L-seryl)-sulfamoyl)N3-methyluridine
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ESRF BEAMLINE ID23-1 |
Synchrotron site | ESRF |
Beamline | ID23-1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2017-12-17 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.972422 |
Spacegroup name | P 43 21 2 |
Unit cell lengths | 83.721, 83.721, 228.419 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 67.520 - 2.270 |
R-factor | 0.214 |
Rwork | 0.213 |
R-free | 0.22300 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | Model generated from structure 2DQ3 |
RMSD bond length | 0.010 |
RMSD bond angle | 1.100 |
Data reduction software | XDS |
Data scaling software | Aimless (0.6.2) |
Phasing software | PHASER (1.13-2998) |
Refinement software | BUSTER (2.10.3) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 76.140 | 76.140 | 2.090 |
High resolution limit [Å] | 1.980 | 6.260 | 1.980 |
Rmerge | 0.084 | 0.032 | 2.339 |
Rmeas | 0.089 | 0.035 | 2.480 |
Rpim | 0.030 | 0.012 | 0.817 |
Total number of observations | 497991 | ||
Number of reflections | 57726 | 2087 | 8251 |
<I/σ(I)> | 12.1 | ||
Completeness [%] | 99.9 | 100 | 99.8 |
Redundancy | 8.6 | 7.4 | 9.1 |
CC(1/2) | 0.999 | 0.999 | 0.712 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | Holo protein, concentrated to 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 5 mM DTT, was mixed with an equal volume of 7.5% w/v PEG 8000, 50 mM CaCl2, 20% v/v ethylene glycol, 100 mM Morpheus buffer system 1 (MES/Imidazole) pH 6.5. Suitable crystals were soaked with 2 mM compound in a similar crystallization solution containing a 10% w/v PEG 8000. |