6NDR
Crystal structure of dTDP-6-deoxy-D-glucose-3,5-epimerase RmlC from Legionella pneumophila Philadelphia 1 in complex with dTDP-4-KETO-L-RHAMNOSE
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | ROTATING ANODE |
Source details | RIGAKU FR-E+ SUPERBRIGHT |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2017-11-26 |
Detector | RIGAKU SATURN 944+ |
Wavelength(s) | 1.5418 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 103.380, 46.160, 102.030 |
Unit cell angles | 90.00, 112.29, 90.00 |
Refinement procedure
Resolution | 47.202 - 1.600 |
R-factor | 0.1514 |
Rwork | 0.150 |
R-free | 0.17630 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2ixi as per MorDa |
RMSD bond length | 0.009 |
RMSD bond angle | 1.019 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | MoRDa |
Refinement software | PHENIX |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 47.202 | 47.202 | 1.640 |
High resolution limit [Å] | 1.600 | 7.160 | 1.600 |
Rmerge | 0.030 | 0.024 | 0.359 |
Rmeas | 0.033 | 0.026 | 0.442 |
Number of reflections | 57363 | 715 | 3853 |
<I/σ(I)> | 24.2 | 69.54 | 3.02 |
Completeness [%] | 97.0 | 99.2 | 88.9 |
Redundancy | 4.036 | 6.75 | 2.835 |
CC(1/2) | 1.000 | 1.000 | 0.896 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 285 | Microlytic MCSG1 screen, condition E4: 200mM Lithium sulfate, 25% PEG 3350, 100mM Tris base / HCl pH 8.5: LepnA.18372.a.B1.PW38444 at 17.2mg/ml. Cryo: 20% EG: tray: 300303e4g8: puck uhg9-6. |