6D4K
Crystal structure of L,D-transpeptidase 3 from Mycobacterium tuberculosis at 1.32 A resolution
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) |
| Synchrotron site | PETRA III, EMBL c/o DESY |
| Beamline | P13 (MX1) |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2017-07-15 |
| Detector | DECTRIS PILATUS 6M-F |
| Wavelength(s) | 1.000 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 44.122, 46.407, 112.575 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 42.904 - 1.320 |
| R-factor | 0.1776 |
| Rwork | 0.176 |
| R-free | 0.21780 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 4k73 |
| RMSD bond length | 0.005 |
| RMSD bond angle | 0.849 |
| Data reduction software | XDS |
| Data scaling software | Aimless (0.5.27) |
| Phasing software | PHASER |
| Refinement software | PHENIX (1.10.1_2155) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 46.410 | 46.410 | 1.340 |
| High resolution limit [Å] | 1.320 | 7.110 | 1.320 |
| Rmerge | 0.053 | 0.044 | 1.246 |
| Rmeas | 0.056 | 0.047 | 1.294 |
| Rpim | 0.016 | 0.015 | 0.346 |
| Total number of observations | 667060 | ||
| Number of reflections | 54013 | 431 | 2693 |
| <I/σ(I)> | 21.8 | ||
| Completeness [%] | 98.1 | 99.8 | 96.7 |
| Redundancy | 12.3 | 10.1 | 13.5 |
| CC(1/2) | 0.999 | 0.998 | 0.828 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 291 | PEG 8000 10% (w/v), Hepes 100 mM, calcium acetate 200 mM |
