1MXI
Structure of YibK from Haemophilus influenzae (HI0766): a Methyltransferase with a Cofactor Bound at a Site Formed by a Knot
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 17-ID |
Synchrotron site | APS |
Beamline | 17-ID |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2001-10-01 |
Detector | MARRESEARCH |
Wavelength(s) | 1.00 |
Spacegroup name | P 41 21 2 |
Unit cell lengths | 40.800, 40.800, 165.800 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 20.000 - 1.700 |
Rwork | 0.196 |
R-free | 0.25400 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | PDB 1j85 |
RMSD bond length | 0.017 |
RMSD bond angle | 1.800 |
Data reduction software | DENZO |
Data scaling software | SCALEPACK |
Phasing software | CNS |
Refinement software | CNS |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 50.000 | 1.780 |
High resolution limit [Å] | 1.700 | 1.700 |
Rmerge | 0.040 | 0.223 |
Total number of observations | 281315 * | |
Number of reflections | 15394 | |
<I/σ(I)> | 18.5 | |
Completeness [%] | 93.7 | 69.2 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | Vapor diffusion, hanging drop * | 7.5 * | 298 | 20% PMME 2000, 0.1 M sodium acetate, 0.2 M ammonium acetate, 3 % ethylene glycol, pH 4.6, Vapor diffusion, hanging drop, soaking of crystal with cofactor SAH, temperature 298K |
Crystallization Reagents in Literatures
ID | crystal ID | solution | reagent name | concentration (unit) | details |
1 | 1 | drop | protein | 12 (mg/ml) | |
2 | 1 | drop | Tris-HCl | 50 (mM) | pH7.5 |
3 | 1 | drop | dithiothreitol | 0.1 (mM) | |
4 | 1 | drop | EDTA | 0.1 (mM) | |
5 | 1 | reservoir | PEG2000MME | 20 (%) | |
6 | 1 | reservoir | sodium acetate | 0.1 (M) | pH4.6 |
7 | 1 | reservoir | ammonium acetate | 0.2 (M) | |
8 | 1 | reservoir | ethylene glycol | 3 (%) |