6UK3
Crystal Structure of S-adenosyl-L-homocysteine hydrolase from Acanthamoeba castellanii with bound NAD and Adenosine
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 21-ID-F |
Synchrotron site | APS |
Beamline | 21-ID-F |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2019-08-01 |
Detector | RAYONIX MX-300 |
Wavelength(s) | 0.97872 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 96.030, 112.730, 105.920 |
Unit cell angles | 90.00, 114.72, 90.00 |
Refinement procedure
Resolution | 50.000 - 1.400 |
R-factor | 0.1301 |
Rwork | 0.130 |
R-free | 0.16110 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5v96 |
RMSD bond length | 0.005 |
RMSD bond angle | 0.862 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER (2.8.3) |
Refinement software | PHENIX (1.17rc1_3602) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 1.440 |
High resolution limit [Å] | 1.400 | 6.260 | 1.400 |
Rmerge | 0.044 | 0.025 | 0.584 |
Rmeas | 0.050 | 0.030 | 0.670 |
Number of reflections | 400199 | 4528 | 29495 |
<I/σ(I)> | 16.63 | 45.58 | 2.2 |
Completeness [%] | 99.7 | 97.3 | 99.5 |
Redundancy | 4.142 | 3.887 | 4.125 |
CC(1/2) | 0.999 | 0.998 | 0.801 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 287 | AccaA.00032.a.B1.PW38645 at 20.81 mg/ml, incubated with 2 mM NAD, SAH, mixed 1:1 with 12.5% (w/v) PEG-1000, 12.5% (w/v) PEG-3350, 12.5% (v/v) MPD, 0.1 M MOPS/HEPES-Na, pH=7.5, 0.02 M of sodium formate, ammonium acetate, trisodium citrate, sodium potassium L-tartrate, 0.2 M sodium oxamate. Tray: 311079g8, puck: ved0-8 |