8GRD
Crystal structure of a constitutively active mutant of the alpha beta heterodimer of human IDH3 in complex with ADP and Mg
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRF BEAMLINE BL17U1 |
Synchrotron site | SSRF |
Beamline | BL17U1 |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2021-05-11 |
Detector | ADSC QUANTUM 315r |
Wavelength(s) | 0.9785 |
Spacegroup name | I 4 2 2 |
Unit cell lengths | 165.897, 165.897, 129.583 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 23.313 - 2.699 |
R-factor | 0.1965 |
Rwork | 0.194 |
R-free | 0.24180 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6kdf |
RMSD bond length | 0.009 |
RMSD bond angle | 1.041 |
Data reduction software | HKL-2000 |
Data scaling software | HKL-2000 |
Phasing software | PHENIX (1.17.1_3660) |
Refinement software | PHENIX (1.17.1_3660) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 2.750 |
High resolution limit [Å] | 2.699 | 7.320 | 2.700 |
Rmerge | 0.149 | 0.042 | 1.086 |
Rmeas | 0.152 | 0.043 | 1.107 |
Rpim | 0.029 | 0.009 | 0.216 |
Number of reflections | 25101 | 1372 | 1230 |
<I/σ(I)> | 3 | ||
Completeness [%] | 100.0 | 100 | 99.9 |
Redundancy | 26.3 | 23.5 | 26 |
CC(1/2) | 0.999 | 0.904 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.1 | 293 | 0.1 M sodium cacodylate (pH 5.1), 0.1 M calcium acetate, 10% (w/v) PEG 8000, 4 mM ADP, 4 mM CIT and 0.4 mM MgCl2 |