5V96
Crystal Structure of S-adenosyl-l-homocysteine Hydrolase from Naegleria fowleri 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 | 2017-02-24 |
Detector | MARMOSAIC 300 mm CCD |
Wavelength(s) | 0.97872 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 69.830, 134.330, 239.790 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 48.408 - 2.000 |
R-factor | 0.1388 |
Rwork | 0.138 |
R-free | 0.17970 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3ond |
RMSD bond length | 0.007 |
RMSD bond angle | 0.868 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | MoRDa |
Refinement software | PHENIX |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 48.408 | 48.408 | 2.050 |
High resolution limit [Å] | 2.000 | 8.940 | 2.000 |
Rmerge | 0.093 | 0.031 | 0.498 |
Rmeas | 0.101 | 0.034 | 0.543 |
Number of reflections | 152740 | 1878 | 11197 |
<I/σ(I)> | 16.01 | 42.48 | 3.89 |
Completeness [%] | 99.9 | 98.1 | 100 |
Redundancy | 6.244 | 5.51 | 6.286 |
CC(1/2) | 0.998 | 0.998 | 0.903 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 290 | NafoA.00032.a.B1.PW37932 at 19.8 mg/ml incubated with 3 mM each SAH and NAD, then mixed 1:1 with an equal volume JCSG+(c4): 10% (w/v) PEG-6000, 0.1 M HEPES free acid/NaOH, pH = 7.0, cryoprotected with 20% ethylene glycol |