4QGG
TMK in complex with compound 46, 2-(3-CHLOROPHENOXY)-3-FLUORO-4-{(1R)-3-METHYL-1-[(3S)-3-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)PIPERIDIN-1-YL]BUTYL}BENZOIC ACID
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 17-ID |
Synchrotron site | APS |
Beamline | 17-ID |
Temperature [K] | 140 |
Detector technology | PIXEL |
Collection date | 2010-08-16 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 1.0 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 46.996, 91.042, 48.504 |
Unit cell angles | 90.00, 100.63, 90.00 |
Refinement procedure
Resolution | 47.670 - 1.620 |
R-factor | 0.2087 |
Rwork | 0.208 |
R-free | 0.22220 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.010 |
RMSD bond angle | 1.060 |
Data reduction software | PROCESS |
Data scaling software | SCALA (3.3.16) |
Phasing software | AMoRE |
Refinement software | BUSTER-TNT (BUSTER 2.11.5) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 91.042 | 91.042 | 1.710 |
High resolution limit [Å] | 1.621 | 5.130 | 1.620 |
Rmerge | 0.020 | 0.483 | |
Total number of observations | 5270 | 24954 | |
Number of reflections | 49913 | ||
<I/σ(I)> | 15.7 | 26.1 | 1.6 |
Completeness [%] | 98.4 | 98.2 | 98.2 |
Redundancy | 3.4 | 3.2 | 3.4 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | To obtain the inhibitor bound crystal form of TMK-S.aureus crystals were initially grown in the absence of compound using the sitting drop method at 293 K with a reservoir solution of 100 mM PCPT (propionate-cacodylate-bistris propane buffer) pH 7-8, 21-24% PEG 3350, 200 mM Mg2Cl using 1:1 protein:reservoir solution with the protein solution at 13 mg/mL. Crystals were harvested and soaked overnight in a solution containing 100 mM PCPT, 35% PEG 3350, 200 mM Mg2Cl and 1-2 mM or compound from a 100 mM DMSO stock. After soaking the crystals were cryoprotected by soaking for 15 minutes in compound-soak solution supplemented with 20% ethylene glycol., VAPOR DIFFUSION, SITTING DROP |