7HKV

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 Z300245038 (DNV2_NS5A-x0749)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
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

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.387	α = 90
b = 116.009	β = 90
c = 147.848	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 XE 9M		2023-12-05		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92124	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.86	58.04	99.9	0.305	0.317	0.085	0.997	6.2	13.7		59708

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.9		97.7	7.634	7.923	2.109	0.326		13.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5K5M	1.86	58.07	54149	2973	95.56	0.20502	0.20242	0.25148	RANDOM	56.304

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-3.54			0.7		2.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.933
r_dihedral_angle_3_deg	18.285
r_dihedral_angle_4_deg	17.643
r_long_range_B_refined	10.909
r_long_range_B_other	10.684
r_scangle_other	7.309
r_dihedral_angle_1_deg	7.041
r_mcangle_it	6.495
r_mcangle_other	6.494
r_scbond_it	4.584
r_scbond_other	4.583
r_mcbond_other	4.074
r_mcbond_it	4.032
r_angle_refined_deg	1.543
r_angle_other_deg	1.243
r_chiral_restr	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4759
Nucleic Acid Atoms
Solvent Atoms	434
Heterogen Atoms	71

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC5	refinement
Aimless	data scaling
PHASER	phasing
XDS	data reduction