5VXJ
2.50 A resolution structure of IpaD from Shigella flexneri in complex with single-domain antibody JMK-E3
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 | 2016-08-14 |
| Detector | DECTRIS PILATUS 6M |
| Wavelength(s) | 1.000 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 79.014, 163.350, 216.021 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 45.048 - 2.500 |
| R-factor | 0.1995 |
| Rwork | 0.196 |
| R-free | 0.25900 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 2j0o |
| RMSD bond length | 0.002 |
| RMSD bond angle | 0.477 |
| Data scaling software | Aimless (0.5.27) |
| Phasing software | PHASER |
| Refinement software | PHENIX (1.12rc1_2803) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 48.620 | 48.620 | 2.540 |
| High resolution limit [Å] | 2.500 | 13.690 | 2.500 |
| Rmerge | 0.145 | 0.039 | 1.213 |
| Rmeas | 0.157 | 0.043 | 1.312 |
| Rpim | 0.060 | 0.018 | 0.495 |
| Total number of observations | 651001 | 4297 | 33653 |
| Number of reflections | 96196 | ||
| <I/σ(I)> | 10.8 | 33.8 | 2 |
| Completeness [%] | 98.6 | 97.8 | 100 |
| Redundancy | 6.8 | 6.3 | 7 |
| CC(1/2) | 0.996 | 0.991 | 0.683 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293 | 0.2 M Trimethylamine N-oxide dehydrate, 0.1 M Tris-HCl (pH 8.5), 20% (w/v) PEG 2000 |
