7QPE
Crystal structure of serine hydroxymethyltransferase, isoform 6 from Arabidopsis thaliana (SHM6)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) |
Synchrotron site | PETRA III, EMBL c/o DESY |
Beamline | P14 (MX2) |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-10-20 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.9763 |
Spacegroup name | P 64 2 2 |
Unit cell lengths | 129.683, 129.683, 302.305 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 63.400 - 2.180 |
R-factor | 0.2081 |
Rwork | 0.208 |
R-free | 0.23000 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 7pzz |
RMSD bond length | 0.008 |
RMSD bond angle | 0.948 |
Data reduction software | XDS |
Data scaling software | STARANISO |
Phasing software | PHASER |
Refinement software | PHENIX (1.19_4092) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 105.280 | 105.280 | 2.430 |
High resolution limit [Å] | 2.180 | 7.230 | 2.180 |
Rmerge | 0.077 | 0.031 | 2.180 |
Number of reflections | 49107 | 2454 | 2456 |
<I/σ(I)> | 29.8 | 95.5 | 2.2 |
Completeness [%] | 62.0 | 99.9 | 11.4 |
Redundancy | 38.5 | 33.1 | 34.4 |
CC(1/2) | 0.999 | 0.999 | 0.825 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.3 | 292 | 0.18 M Ammonium nitrate, 0.09 M Sodium cacodylate 5.3, 20% v/v PEG Smear Low, 10% Ethylene glycol (based on the D1 condition of the BCS screen, Molecular Dimensions). Cryoprotection was obtained by increasing the ethylene glycol concentration to 20 % in the drop with crystals. |