9DT8
Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (ADP bound, Orthorhombic P)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | NSLS-II BEAMLINE 19-ID |
Synchrotron site | NSLS-II |
Beamline | 19-ID |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2024-03-24 |
Detector | DECTRIS EIGER2 XE 9M |
Wavelength(s) | 0.9786 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 57.316, 79.485, 91.372 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 59.970 - 1.150 |
R-factor | 0.1372 |
Rwork | 0.136 |
R-free | 0.15590 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.007 |
RMSD bond angle | 1.086 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | PHENIX ((dev_5295: ???)) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 79.480 | 1.180 |
High resolution limit [Å] | 1.150 | 1.150 |
Rmerge | 0.048 | 0.398 |
Rmeas | 0.050 | 0.491 |
Rpim | 0.014 | 0.279 |
Total number of observations | 1374944 | 4144 |
Number of reflections | 112731 | 1608 |
<I/σ(I)> | 25.5 | 2.2 |
Completeness [%] | 76.1 | |
Redundancy | 12.2 | 2.6 |
CC(1/2) | 1.000 | 0.801 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 291 | 25% (v/v) PEG 3350, 0.2M sodium acetate, 0.1 M Tris 8.4, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. plate Liu-S-107 CD/34. 5 hour soak in 2mM NAD, Puck: PSL-1608, Cryo: 30% (v/v) PEG 3350, 0.2 M sodium acetate, 0.1 M Tris 8.4. |