6D5A
Crystal structure of L,D-transpeptidase 5 from Mycobacterium tuberculosis in apo form
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | LNLS BEAMLINE W01B-MX2 |
| Synchrotron site | LNLS |
| Beamline | W01B-MX2 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2017-05-30 |
| Detector | DECTRIS PILATUS 2M |
| Wavelength(s) | 1.458 |
| Spacegroup name | P 62 2 2 |
| Unit cell lengths | 97.446, 97.446, 193.972 |
| Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
| Resolution | 43.538 - 2.622 |
| R-factor | 0.2087 |
| Rwork | 0.206 |
| R-free | 0.26080 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 5du7 |
| RMSD bond length | 0.010 |
| RMSD bond angle | 1.154 |
| 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] | 43.540 | 43.540 | 2.740 |
| High resolution limit [Å] | 2.620 | 9.080 | 2.620 |
| Rmerge | 0.115 | 0.041 | 0.896 |
| Rmeas | 0.126 | 0.046 | 0.983 |
| Rpim | 0.048 | 0.020 | 0.380 |
| Total number of observations | 85436 | ||
| Number of reflections | 15940 | 440 | 1878 |
| <I/σ(I)> | 9.7 | ||
| Completeness [%] | 94.2 | 86.3 | 93.8 |
| Redundancy | 5.4 | 4.4 | 5.3 |
| CC(1/2) | 0.995 | 0.993 | 0.741 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 291 | PEG 4000 22% (w/v), sodium acetate 100 mM, ammonium sulphate 200 mM |
