7DBT
Crystal structure of catalytic domain of Anhydrobiosis-related Mn-dependent Peroxidase (AMNP) from Ramazzottius varieornatus (Mn2+-bound form)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SPRING-8 BEAMLINE BL44XU |
Synchrotron site | SPring-8 |
Beamline | BL44XU |
Temperature [K] | 95 |
Detector technology | PIXEL |
Collection date | 2020-07-20 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 1.2500 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 48.400, 41.160, 79.768 |
Unit cell angles | 90.00, 92.00, 90.00 |
Refinement procedure
Resolution | 19.930 - 2.300 |
R-factor | 0.2648 |
Rwork | 0.262 |
R-free | 0.32510 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 7dbu |
RMSD bond length | 0.008 |
RMSD bond angle | 1.187 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | MOLREP |
Refinement software | PHENIX ((1.11.1_2575: ???)) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 42.090 | 2.380 |
High resolution limit [Å] | 2.300 | 2.300 |
Rmerge | 0.160 | 0.547 |
Number of reflections | 14127 | 1337 |
<I/σ(I)> | 4.6 | 1.7 |
Completeness [%] | 98.6 | 48.4 |
Redundancy | 4.4 | 4.2 |
CC(1/2) | 0.987 | 0.866 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | Crystallization: 10% PEG3350, 100 mM imidazole-HCl buffer (pH 7.5), 300 mM zinc acetate, and 50 mM sodium fluoride Soaking: 11% PEG3350, 100 mM imidazole-HCl buffer (pH 7.5), 50 mM manganese chloride, and 50 mM sodium fluoride |