6XEP
Crystal structure of Thiamine-monophosphate kinase from Stenotrophomonas maltophilia K279a
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | ROTATING ANODE |
Source details | RIGAKU FR-E+ SUPERBRIGHT |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2020-05-28 |
Detector | RIGAKU SATURN 944+ |
Wavelength(s) | 1.5418 |
Spacegroup name | P 21 21 2 |
Unit cell lengths | 80.440, 88.810, 44.270 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 44.410 - 1.800 |
R-factor | 0.1683 |
Rwork | 0.166 |
R-free | 0.20410 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5cm7 |
RMSD bond length | 0.007 |
RMSD bond angle | 0.898 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | PHENIX (1.18.2) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 1.850 |
High resolution limit [Å] | 1.800 | 8.050 | 1.800 |
Rmerge | 0.055 | 0.027 | 0.619 |
Rmeas | 0.056 | 0.028 | 0.645 |
Number of reflections | 29881 | 400 | 2091 |
<I/σ(I)> | 36.36 | 103.57 | 4.39 |
Completeness [%] | 99.1 | 99.5 | 95.1 |
Redundancy | 19.233 | 23.642 | 12.142 |
CC(1/2) | 0.999 | 0.998 | 0.926 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | Microlytic MCSG-1 screen, condition H10: 25% PEG 3350, 100mM HEPES free acid / Sodium hydroxide pH 7.5: StmaA.17905.a.B1.PW38774 at 19mg/ml. the crystal was soaked for 1h with 2.5mM Thiamine monophosphate and AMPPNP, neither is visible in the electron density; tray: 315043h10: cryo: soak + 15% EG: puck: jfm9-1. |