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 |