6RQA
Crystal structure of the iminosuccinate reductase of Paracoccus denitrificans in complex with NAD+
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 | 2019-05-03 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.97625 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 50.386, 72.407, 164.266 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 29.400 - 2.560 |
R-factor | 0.1813 |
Rwork | 0.176 |
R-free | 0.22500 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1omo |
RMSD bond length | 0.004 |
RMSD bond angle | 0.517 |
Data reduction software | XDS |
Data scaling software | SCALA (3.3.22) |
Phasing software | PHENIX |
Refinement software | PHENIX |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 29.400 | 29.401 | 2.700 |
High resolution limit [Å] | 2.560 | 8.100 | 2.560 |
Rmerge | 0.097 | 0.042 | 0.527 |
Rmeas | 0.105 | 0.046 | 0.573 |
Rpim | 0.041 | 0.019 | 0.224 |
Total number of observations | 3817 | 18723 | |
Number of reflections | 20152 | 713 | 2893 |
<I/σ(I)> | 12.6 | 28.7 | 3.3 |
Completeness [%] | 99.9 | 98 | 100 |
Redundancy | 6.5 | 5.4 | 6.5 |
CC(1/2) | 0.998 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.9 | 289 | His-tagged iminosuccinate reductase (10 mg/ml) in buffer containing 25 mM Tris-HCl (pH 8.0), 100 mM NaCl, 1 mM MgCl2, 0.1 mM DTT, 5 mM Tb-Xo4, and 5 mM NAD+ was mixed in a ratio of 1:1 with crystallization buffer containing 200 mM Mg(NO3)2 and 20% (w/v) PEG3350 (pH 5.9). |