8KA0
Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin and a nicotinamide adenine dinucleotide (NAD+)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PAL/PLS BEAMLINE 5C (4A) |
Synchrotron site | PAL/PLS |
Beamline | 5C (4A) |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2022-03-24 |
Detector | DECTRIS EIGER X 9M |
Wavelength(s) | 1.000 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 136.222, 48.931, 178.603 |
Unit cell angles | 90.00, 95.70, 90.00 |
Refinement procedure
Resolution | 29.620 - 2.350 |
R-factor | 0.22 |
Rwork | 0.217 |
R-free | 0.26300 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 8k9z |
RMSD bond length | 0.011 |
RMSD bond angle | 1.033 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | MOLREP |
Refinement software | REFMAC (5.8.0415) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 29.620 | 2.390 |
High resolution limit [Å] | 2.350 | 2.350 |
Number of reflections | 98734 | 4831 |
<I/σ(I)> | 11.6 | |
Completeness [%] | 99.8 | 99.9 |
Redundancy | 6.9 | |
CC(1/2) | 0.999 | 0.675 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293 | 0.1 M Tris-HCl (pH 8.5), 32.5% (w/v) PEG 4000 and 0.15 M sodium acetate. 10 mM NAD+ soaking |