7HKD

Group deposition for crystallographic fragment screening of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 -- Crystal structure of the NS5 RNA-dependent RNA polymerase from Dengue virus serotype 2 in complex with Z53825479 (DNV2_NS5A-x0172)

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	DIAMOND BEAMLINE I04-1
Synchrotron site	Diamond
Beamline	I04-1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-08-08
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.92124
Spacegroup name	I 2 2 2
Unit cell lengths	82.494, 116.353, 148.188
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	74.200 - 1.660
R-factor	0.18821
Rwork	0.187
R-free	0.21393
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5k5m
RMSD bond length	0.009
RMSD bond angle	1.523
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	REFMAC (5.8.0267)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	74.090	1.690
High resolution limit [Å]	1.660	1.660
Rmerge	0.146	5.521
Rmeas	0.152	5.800
Rpim	0.041	1.762
Total number of observations	1120117	43614
Number of reflections	84143	4087
<I/σ(I)>	10.1	0.3
Completeness [%]	100.0
Redundancy	13.3	10.7
CC(1/2)	0.999	0.305

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293.15	350 mM Magnesium chloride, 10% PEG 4000, 100 mM MES, pH 6.5