7AP1
Klebsiella pneumoniae Seryl-tRNA synthetase in Complex with Compound SerS7HMDDA
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SOLEIL BEAMLINE PROXIMA 1 |
Synchrotron site | SOLEIL |
Beamline | PROXIMA 1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2017-10-01 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.991870 |
Spacegroup name | P 43 21 2 |
Unit cell lengths | 84.670, 84.670, 229.865 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 19.960 - 2.180 |
R-factor | 0.2012 |
Rwork | 0.200 |
R-free | 0.22590 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6h9x |
RMSD bond length | 0.008 |
RMSD bond angle | 0.950 |
Data reduction software | XDS |
Data scaling software | Aimless (0.7.4) |
Phasing software | PHASER |
Refinement software | BUSTER (2.10.3 (18-SEP-2020)) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 19.960 | 19.960 | 2.010 |
High resolution limit [Å] | 1.910 | 6.040 | 1.910 |
Rmerge | 0.105 | 0.044 | 4.007 |
Rmeas | 0.110 | 0.046 | 4.176 |
Rpim | 0.032 | 0.014 | 1.170 |
Total number of observations | 805160 | 24582 | 119554 |
Number of reflections | 65882 | 2278 | 9463 |
<I/σ(I)> | 10.7 | 38.9 | 0.6 |
Completeness [%] | 99.8 | 97.3 | 99.6 |
Redundancy | 12.2 | 10.8 | 12.6 |
CC(1/2) | 0.999 | 0.999 | 0.756 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | Holo protein at 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 5 mM synthesized compound in the same crystallization solution but containing a 10% w/v PEG 8000 concentration. |