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.