6ZFN
Structure of an inactive E404Q variant of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with 1-methyl alpha-1,2-mannobiose
This is a non-PDB format compatible entry.
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I03 |
Synchrotron site | Diamond |
Beamline | I03 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-01-20 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.97625 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 42.752, 81.680, 52.994 |
Unit cell angles | 90.00, 92.93, 90.00 |
Refinement procedure
Resolution | 52.920 - 1.100 |
Rwork | 0.106 |
R-free | 0.12790 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6zdf |
RMSD bond length | 0.018 |
RMSD bond angle | 2.077 |
Data reduction software | DIALS (1.8.3-g908a951f-release) |
Data scaling software | Aimless (0.6.1) |
Phasing software | PHASER (2.7.17) |
Refinement software | REFMAC (5.8.0258) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 52.920 | 1.120 |
High resolution limit [Å] | 1.100 | 1.100 |
Rmerge | 0.054 | 0.223 |
Rmeas | 0.061 | 0.271 |
Rpim | 0.029 | 0.150 |
Number of reflections | 143298 | 5215 |
<I/σ(I)> | 11.9 | 3.3 |
Completeness [%] | 97.6 | 71.3 |
Redundancy | 3.7 | 2.6 |
CC(1/2) | 0.998 | 0.944 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 279 | 100 mM sodium acetate pH 4.6, 200 mM ammonium sulfate, 12.8% PEG-MME 2000. Protein at 10 mg/ml in 25 mM HEPES pH 7.0, 200 mM NaCl buffer with 2.3 mM GlcMan4OMe (10 x molar ratio). 500 nl protein solution and 500 nl reservoir solution. |