7Y4K
Crystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)glycyl-L-phenylalanyl-N6-((benzyloxy)carbonyl)-L-ornitine
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PHOTON FACTORY BEAMLINE BL-5A |
Synchrotron site | Photon Factory |
Beamline | BL-5A |
Temperature [K] | 95 |
Detector technology | PIXEL |
Collection date | 2020-02-22 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 1.0 |
Spacegroup name | P 41 21 2 |
Unit cell lengths | 67.639, 67.639, 141.079 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 48.820 - 1.700 |
R-factor | 0.2081 |
Rwork | 0.207 |
R-free | 0.23000 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4huo |
RMSD bond length | 0.008 |
RMSD bond angle | 1.163 |
Data reduction software | XDS |
Data scaling software | SCALA (3.3.22) |
Phasing software | MOLREP |
Refinement software | REFMAC (5.8.0131) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 60.991 | 45.296 | 1.790 |
High resolution limit [Å] | 1.700 | 5.380 | 1.700 |
Rmerge | 0.020 | 0.749 | |
Rmeas | 0.056 | 0.021 | 0.788 |
Rpim | 0.016 | 0.006 | 0.241 |
Total number of observations | 462557 | 15514 | 55498 |
Number of reflections | 36955 | 1348 | 5269 |
<I/σ(I)> | 27.9 | 80.8 | 3.3 |
Completeness [%] | 100.0 | 99.8 | 100 |
Redundancy | 12.5 | 11.5 | 10.5 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 4 | 296 | PEG 2000, Lithium sulfate, Sodium acetate |