6E58
Crystal structure of Streptococcus pyogenes endo-beta-N-acetylglucosaminidase (EndoS2)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRL BEAMLINE BL12-2 |
Synchrotron site | SSRL |
Beamline | BL12-2 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2017-05-11 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.979460 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 89.169, 105.829, 259.275 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 38.887 - 2.750 |
R-factor | 0.2121 |
Rwork | 0.209 |
R-free | 0.26400 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4nuy |
RMSD bond length | 0.009 |
RMSD bond angle | 1.104 |
Data reduction software | XDS |
Data scaling software | Aimless (0.7.1) |
Phasing software | MOLREP |
Refinement software | PHENIX (1.10.1_2155) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 38.890 | 38.890 | 2.820 |
High resolution limit [Å] | 2.750 | 12.600 | 2.750 |
Rmerge | 0.171 | 0.057 | 0.853 |
Rmeas | 0.204 | 0.068 | 1.033 |
Rpim | 0.108 | 0.035 | 0.569 |
Total number of observations | 193715 | ||
Number of reflections | 60381 | 674 | 4302 |
<I/σ(I)> | 6.1 | ||
Completeness [%] | 93.9 | 89.8 | 95.7 |
Redundancy | 3.2 | 3.2 | 3 |
CC(1/2) | 0.975 | 0.993 | 0.363 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 298 | 250 nL 7 mg/mL wild-type EndoS2 + 250 nL mother liquor (0.2 M sodium citrate tribasic, 0.1 M sodium citrate, pH 4, 20% w/v PEG3350) in sitting drops, followed by streak seeding into hanging drops (1 mL 6.6 mg/mL protein + 1 mL mother liquor, single plate-like crystals after three days) |