5JXM
Crystal Structure of Prenyltransferase PriB Apo Form
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 31-ID |
Synchrotron site | APS |
Beamline | 31-ID |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2015-07-09 |
Detector | RAYONIX MX225HE |
Wavelength(s) | 0.97931 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 103.526, 83.723, 41.527 |
Unit cell angles | 90.00, 106.27, 90.00 |
Refinement procedure
Resolution | 27.555 - 1.150 |
R-factor | 0.1792 |
Rwork | 0.179 |
R-free | 0.21080 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5inj |
RMSD bond length | 0.018 |
RMSD bond angle | 1.516 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | AutoSol |
Refinement software | PHENIX (1.10_2155) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 49.691 | 49.691 | 1.150 |
High resolution limit [Å] | 1.080 | 3.240 | 1.080 |
Rmerge | 0.069 | 0.038 | 2.602 |
Number of reflections | 131276 | ||
<I/σ(I)> | 8.15 | 32.1 | 0.32 |
Completeness [%] | 90.6 | 98.6 | 51.9 |
Redundancy | 3.5 | ||
CC(1/2) | 0.998 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293.15 | PriB was crystallized by sitting drop vapor diffusion method by 1:1 v/v mixing of 10 mg/mL PriB solution in the presence of 1 mM L-Tryptophan and 1 mM daptomycin with reservoir solution containing 0.1 M Tris pH 8.5, 20% w/v PEG 3350, 0.1 M MgCl2. The mixed drops of 0.4-1 uL were equilibrated over a reservoir solution of 50 uL and incubated at 20oC in the dark. The iodine derivative was prepared by 1:3 v/v soaking a solution of 0.5 M sodium iodide, 0.05 M Tris pH 8.5, 10% w/v PEG 3350, 0.05 M MgCl2 into PriB crystals |