7HKP

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 Z1198279205 (DNV2_NS5A-x0414)

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	2023-12-03
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.92124
Spacegroup name	I 2 2 2
Unit cell lengths	82.344, 115.570, 147.292
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	49.630 - 2.120
R-factor	0.20563
Rwork	0.202
R-free	0.27037
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5k5m
RMSD bond length	0.005
RMSD bond angle	1.380
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]	49.580	2.180
High resolution limit [Å]	2.120	2.120
Rmerge	0.436	6.224
Rmeas	0.453	6.455
Rpim	0.122	1.706
Total number of observations	548985	45372
Number of reflections	40123	3191
<I/σ(I)>	5.5	0.5
Completeness [%]	99.8
Redundancy	13.7	14.2
CC(1/2)	0.994	0.330

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