11WX

Crystal Structure of ribosomal large subunit pseudouridine synthase D from Neisseria gonorrhoea

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 19-ID
Synchrotron site	NSLS-II
Beamline	19-ID
Temperature [K]	100
Detector technology	PIXEL
Collection date	2026-02-06
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	C 1 2 1
Unit cell lengths	132.552, 88.011, 101.659
Unit cell angles	90.00, 95.18, 90.00

Refinement procedure

Resolution	44.010 - 1.910
R-factor	0.1692
Rwork	0.168
R-free	0.19310
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.010
RMSD bond angle	1.002
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX (2.0_5936)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	44.010	1.940
High resolution limit [Å]	1.910	1.910
Rmerge	0.055	1.368
Rmeas	0.060	1.477
Rpim	0.023	0.551
Total number of observations	620626	32287
Number of reflections	89815	4577
<I/σ(I)>	18	1.6
Completeness [%]	99.6
Redundancy	6.9	7.1
CC(1/2)	1.000	0.802

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7	291	Index B12L 2.8 M Sodium acetate. NegoA.19228.a.B2.PW39479 at 18.4 mg/mL. 5 mM Uridine 5'-monophosphate disodium salt (UMP) added prior to crystallization but no electron density was observed for these. plate 20669 B12 drop 2, Puck: PSL-0811, Cryo: 75% crystallant + 25% glycerol