6MDV
Crystal structure of Streptococcus pyogenes endo-beta-N-acetylglucosaminidase (EndoS2) with high-mannose glycan
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 17-ID |
| Synchrotron site | APS |
| Beamline | 17-ID |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2017-07-07 |
| Detector | DECTRIS PILATUS 6M |
| Wavelength(s) | 1.033190 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 88.966, 105.353, 257.298 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 29.627 - 2.500 |
| R-factor | 0.2007 |
| Rwork | 0.198 |
| R-free | 0.24830 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 6e58 |
| RMSD bond length | 0.009 |
| RMSD bond angle | 1.157 |
| Data reduction software | XDS |
| Data scaling software | Aimless (0.5.32) |
| Phasing software | PHASER |
| Refinement software | PHENIX (1.10.1_2155) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 29.660 | 29.660 | 2.550 |
| High resolution limit [Å] | 2.500 | 13.230 | 2.500 |
| Rmerge | 0.153 | 0.044 | 1.402 |
| Rmeas | 0.167 | 0.049 | 1.529 |
| Rpim | 0.067 | 0.020 | 0.605 |
| Total number of observations | 507629 | ||
| Number of reflections | 84474 | 608 | 4438 |
| <I/σ(I)> | 9 | ||
| Completeness [%] | 99.9 | 91.5 | 100 |
| Redundancy | 6 | 5.6 | 6.2 |
| CC(1/2) | 0.995 | 0.998 | 0.489 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 4 | 298 | 0.2 M sodium citrate tribasic, 0.1 M sodium citrate, pH 4, 20% w/v PEG3350 |
