5EPE
Crystal structure of SAM-dependent methyltransferase from Thiobacillus denitrificans in complex with S-Adenosyl-L-homocysteine
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 21-ID-G |
Synchrotron site | APS |
Beamline | 21-ID-G |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2015-04-16 |
Detector | MARMOSAIC 300 mm CCD |
Wavelength(s) | 0.97856 |
Spacegroup name | F 2 3 |
Unit cell lengths | 157.536, 157.536, 157.536 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 50.000 - 1.900 |
R-factor | 0.1371 |
Rwork | 0.136 |
R-free | 0.16710 |
Structure solution method | SAD |
RMSD bond length | 0.017 |
RMSD bond angle | 1.717 |
Data reduction software | HKL-3000 |
Data scaling software | HKL-3000 |
Phasing software | HKL-3000 |
Refinement software | REFMAC (5.8.0107) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 1.930 |
High resolution limit [Å] | 1.900 | 5.160 | 1.900 |
Rmerge | 0.100 | 0.048 | 0.914 |
Rmeas | 0.105 | 0.051 | 0.960 |
Rpim | 0.031 | 0.015 | 0.292 |
Total number of observations | 292403 | ||
Number of reflections | 25623 | ||
<I/σ(I)> | 5.6 | 2 | |
Completeness [%] | 100.0 | 99.7 | 100 |
Redundancy | 11.4 | 10.8 | 10.7 |
CC(1/2) | 0.999 | 0.810 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 9.5 | 289 | 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG II condition #56 (0.1M CHES pH=9.5, 20%w/v PEG 4K) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 1 mg/ml TEV solution at 289 K for 3 hours |