8E5S
X-ray structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter WT in an occluded state
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 24-ID-C |
Synchrotron site | APS |
Beamline | 24-ID-C |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-11-01 |
Detector | DECTRIS EIGER2 X 16M |
Wavelength(s) | 0.984 |
Spacegroup name | P 2 21 21 |
Unit cell lengths | 58.658, 70.850, 98.342 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 41.060 - 2.380 |
R-factor | 0.2107 |
Rwork | 0.206 |
R-free | 0.24890 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6c3i |
Data reduction software | XDS (1.20.1_4487) |
Data scaling software | Aimless (1.20.1_4487) |
Phasing software | PHASER |
Refinement software | PHENIX (1.20.1_4487) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 41.060 | 41.060 | 2.470 |
High resolution limit [Å] | 2.380 | 8.910 | 2.380 |
Rmerge | 0.192 | 0.064 | 1.238 |
Rmeas | 0.218 | 0.072 | 1.416 |
Rpim | 0.099 | 0.031 | 0.663 |
Total number of observations | 71063 | 1405 | 7304 |
Number of reflections | 15678 | 318 | 1666 |
<I/σ(I)> | 7.4 | 21.7 | 1.8 |
Completeness [%] | 93.4 | 87.5 | 95.9 |
Redundancy | 4.5 | 4.4 | 4.4 |
CC(1/2) | 0.987 | 0.996 | 0.377 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | LIPIDIC CUBIC PHASE | 6.7 | 298 | 28% PEG400, 0.1 M MES, pH 6.7, 50 mM succinic acid, pH 6.0, 5 mM spermidine, pH 7.0 |