9Q3C

RNA oligonucleotide containing a 3'-deoxyapio-T

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	MAX IV BEAMLINE BioMAX
Synchrotron site	MAX IV
Beamline	BioMAX
Temperature [K]	100
Detector technology	PIXEL
Collection date	2025-05-30
Detector	DECTRIS EIGER2 XE CdTe 16M
Wavelength(s)	0.918
Spacegroup name	P 1 21 1
Unit cell lengths	48.568, 39.312, 76.246
Unit cell angles	90.00, 94.68, 90.00

Refinement procedure

Resolution	28.770 - 1.400
R-factor	0.2018
Rwork	0.199
R-free	0.25980
Structure solution method	SAD
RMSD bond length	0.013
RMSD bond angle	1.978
Data reduction software	autoPROC
Data scaling software	autoPROC
Phasing software	HKL2Map
Refinement software	PHENIX (1.21.1_5286)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	28.770	1.370
High resolution limit [Å]	1.350	1.350
Rpim		0.956
Number of reflections	74552	2378
<I/σ(I)>	4.98
Completeness [%]	98.3
Redundancy	6.7
CC(1/2)	0.986

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7	294	drops contained 400 nl 1mM RNA and 400 nl of 10% 2-methyl-2,4-pentandiol(MPD), 12 mM spermine 4 HCl, 80 mM KCl, 40 mM sodium cacodylate, pH7.0. Drops equilibrated against 70 microliters 40% MPD.