6B1L
Crystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in complex with inhibitor IMP-0001173
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ALS BEAMLINE 5.0.2 |
Synchrotron site | ALS |
Beamline | 5.0.2 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2017-07-14 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 1.0000 |
Spacegroup name | P 21 21 2 |
Unit cell lengths | 80.030, 81.490, 119.440 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 48.170 - 2.300 |
R-factor | 0.2339 |
Rwork | 0.232 |
R-free | 0.27100 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5v0x |
RMSD bond length | 0.002 |
RMSD bond angle | 0.543 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | PHENIX (1.12_2829) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 48.170 | 48.170 | 2.360 |
High resolution limit [Å] | 2.300 | 10.290 | 2.300 |
Rmerge | 0.058 | 0.022 | 0.517 |
Rmeas | 0.065 | 0.025 | 0.577 |
Total number of observations | 189923 | ||
Number of reflections | 35084 | 449 | 2393 |
<I/σ(I)> | 19.19 | 55.28 | 3.03 |
Completeness [%] | 99.1 | 97.8 | 92.3 |
Redundancy | 5.413 | 4.67 | 4.785 |
CC(1/2) | 0.999 | 0.999 | 0.896 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 290 | PlviB.18219.a.FR2.PS38192 at 13.5 mg/mL was incubated with final concentrations of 0.4 mM Myristoyl-CoA and 0.4 mM IMP-0001173 at 4C for 30 min, then mixed with 1:1 with 0.06M Magnesium chloride hexahydrate: 0.0.06M Calcium chloride dihydrate, 0.1M Tris (base): BICINE pH = 8.5 and 49 % of Precipitant Mix 1 (40% (v/v) PEG 500-MME: 20 % (w/v) PEG 20000), Tray 101d6, puck hr00407-15 |