6WO7
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5-Diphosphoinositol pentakisphosphate (5-IP7), Mg, and Fluoride ion
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 22-ID |
Synchrotron site | APS |
Beamline | 22-ID |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2019-06-08 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 1.0 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 45.365, 59.602, 62.493 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 43.130 - 1.400 |
R-factor | 0.1403 |
Rwork | 0.139 |
R-free | 0.16800 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 2fvv |
RMSD bond length | 0.010 |
RMSD bond angle | 1.814 |
Data reduction software | DENZO |
Data scaling software | HKL-2000 |
Phasing software | PHASER |
Refinement software | REFMAC (5.8.0253) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 1.420 |
High resolution limit [Å] | 1.400 | 3.800 | 1.400 |
Rmerge | 0.075 | 0.047 | 0.637 |
Rmeas | 0.077 | 0.049 | 0.668 |
Rpim | 0.020 | 0.012 | 0.196 |
Total number of observations | 484135 | ||
Number of reflections | 33828 | 1874 | 1457 |
<I/σ(I)> | 9.6 | ||
Completeness [%] | 98.9 | 99.8 | 86.9 |
Redundancy | 14.3 | 15.4 | 10 |
CC(1/2) | 0.996 | 0.933 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 293 | 10% (w/v) PEG 8000, 10% (v/v) isopropanol, 200 mM Li2SO4, 75 mM NaAc, pH 5.5 and 25 mM HEPES, pH 7.0 and soaking in condition of 200 mM LiCl, 20% (w/v) PEG 8000, 20% (v/v) isopropanol, 100 mM HEPES, pH 7.0, 20 mM MgCl2 and 80 mM NaF in present of 2mM 5-IP7 |