5BP9
Crystal structure of SAM-dependent methyltransferase from Bacteroides fragilis 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 | P 21 21 21 |
Unit cell lengths | 41.732, 70.660, 78.743 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 50.000 - 1.500 |
R-factor | 0.1341 |
Rwork | 0.132 |
R-free | 0.17950 |
Structure solution method | SAD |
RMSD bond length | 0.011 |
RMSD bond angle | 1.562 |
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 | 1.530 |
High resolution limit [Å] | 1.500 | 4.070 | 1.500 |
Rmerge | 0.062 | 0.040 | 0.692 |
Rmeas | 0.069 | 0.045 | 0.784 |
Rpim | 0.030 | 0.020 | 0.362 |
Total number of observations | 187562 | ||
Number of reflections | 37846 | ||
<I/σ(I)> | 11.3 | 1.9 | |
Completeness [%] | 98.9 | 97.4 | 98 |
Redundancy | 5 | 4.6 | 4.4 |
CC(1/2) | 0.998 | 0.677 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 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 TOP96 condition #29 (0.2 M Ammonium sulfate, 0.1 M Sodium Cacodylate:HCl pH 6.5, 30% (w/v) PEG 8000) 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 |