7HKK

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 Z802824098 (DNV2_NS5A-x0279)

This is a non-PDB format compatible entry.

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	2023-08-09
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.92124
Spacegroup name	I 2 2 2
Unit cell lengths	82.543, 116.835, 148.382
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	74.300 - 1.660
R-factor	0.19733
Rwork	0.196
R-free	0.22643
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5k5m
RMSD bond length	0.008
RMSD bond angle	1.465
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]	74.170	1.690
High resolution limit [Å]	1.660	1.660
Rmerge	0.121	4.709
Rmeas	0.126	4.948
Rpim	0.034	1.507
Total number of observations	1128740	44302
Number of reflections	84731	4149
<I/σ(I)>	10.9	0.3
Completeness [%]	100.0
Redundancy	13.3	10.7
CC(1/2)	0.999	0.318

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