6WOF
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with inositol hexakisphosphate and Mg, presoaked with 5-IP7, Mg and Fluoride, soaking 20min in the absence of Fluoride.
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 | 2019-07-11 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 1.0 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 46.062, 59.827, 62.729 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 27.790 - 1.600 |
R-factor | 0.1239 |
Rwork | 0.123 |
R-free | 0.14840 |
Structure solution method | FOURIER SYNTHESIS |
RMSD bond length | 0.007 |
RMSD bond angle | 1.550 |
Data reduction software | DENZO |
Data scaling software | SCALEPACK |
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 | 1.630 |
High resolution limit [Å] | 1.600 | 4.340 | 1.600 |
Rmerge | 0.048 | 0.034 | 0.235 |
Rmeas | 0.051 | 0.036 | 0.248 |
Rpim | 0.016 | 0.011 | 0.078 |
Total number of observations | 200552 | ||
Number of reflections | 22702 | 1210 | 1138 |
<I/σ(I)> | 11.9 | ||
Completeness [%] | 97.3 | 93.1 | 99.6 |
Redundancy | 8.8 | 9.2 | 8.9 |
CC(1/2) | 0.999 | 0.989 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 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 solution of 200 mM LiCl, 20% (w/v) PEG 8000, 20% (v/v) isopropanol, 100 mM HEPES, pH 7.0, 80 mM NaF, 20 mM MgCl2 in present of 2mM 5-IP7 for 2 days, and transferred into 200 mM LiCl, 20% (w/v) PEG 8000, 20% (v/v) isopropanol, 100 mM HEPES, pH 7.0, 20 mM MgCl2 for 20 min. |