9E5J

env2 cobalamin riboswitch aptamer domain in complex with ethynyl-4-methoxybenzene-cobalamin

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SEALED TUBE
Source details	RIGAKU MICROMAX-003
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-02-17
Detector	DECTRIS PILATUS 200K
Wavelength(s)	1.54178
Spacegroup name	P 1 21 1
Unit cell lengths	41.489, 78.181, 72.653
Unit cell angles	90.00, 93.78, 90.00

Refinement procedure

Resolution	19.640 - 2.350
R-factor	0.2098
Rwork	0.201
R-free	0.29060
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.010
RMSD bond angle	1.879
Data reduction software	HKL-3000
Data scaling software	HKL-3000
Phasing software	PHASER
Refinement software	PHENIX (1.19.2_4158)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	99.000	99.000	2.390
High resolution limit [Å]	2.350	6.370	2.350
Rmerge	0.043	0.023	0.202
Rmeas	0.061	0.032	0.286
Rpim	0.043	0.023	0.202
Total number of observations	32953
Number of reflections	17386	972	500
<I/σ(I)>	8.3
Completeness [%]	88.9	94.9	50.3
Redundancy	1.9	1.9	1.7
CC(1/2)	0.994	0.998	0.902

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	7	303.15	10% (v/v) (+/-)-2-Methyl-2,4-pentanediol, 40 mM Sodium cacodylate trihydrate (pH 7.0), 12 mM Spermine tetrahydrochloride, 80 mM Potassium chloride, 20 mM Magnesium chloride hexahydrate. Hanging drop. 303.15 K