6WGM
Crystal structure of a marine metagenome TRAP solute binding protein specific for pyroglutamate (Sorcerer II Global Ocean Sampling Expedition, unidentified microbe, scf7180008839099) in complex with co-purified pyroglutamate
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 | 2017-11-08 |
| Detector | RAYONIX MX225HE |
| Wavelength(s) | 0.98 |
| Spacegroup name | P 61 |
| Unit cell lengths | 56.251, 56.251, 193.919 |
| Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
| Resolution | 24.360 - 1.400 |
| R-factor | 0.1516 |
| Rwork | 0.151 |
| R-free | 0.16790 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 2pfz |
| RMSD bond length | 0.005 |
| RMSD bond angle | 0.754 |
| Data reduction software | DENZO (720) |
| Data scaling software | Aimless (0.5.32) |
| Phasing software | PHASER (2.7.17) |
| Refinement software | PHENIX (1.17.1_3660) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 38.900 | 38.900 | 1.420 |
| High resolution limit [Å] | 1.400 | 7.670 | 1.400 |
| Rmerge | 0.110 | 0.052 | 1.789 |
| Rmeas | 0.115 | 0.055 | 0.160 |
| Rpim | 0.034 | 0.018 | 0.562 |
| Number of reflections | 68041 | 416 | 3343 |
| <I/σ(I)> | 12.7 | 1.6 | 12.8 |
| Completeness [%] | 100.0 | 95.2 | 99.9 |
| Redundancy | 11.4 | 9.4 | 11.2 |
| CC(1/2) | 0.998 | 0.995 | 0.785 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 292.15 | 1.1M Malonic Acid, 0.15 M Ammonium Citrate tribasic, 0.072 M Succinic Acid, 0.18 M DL-Malic Acid, 0.24 M Sodium Acetate, 0.3 M Sodium Formate, 0.096 M Ammonium Tartrate Dibasic |
