7I2I | pdb_00007i2i

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 Z1262628644 (DNV2_NS5A-x0472)

X-RAY DIFFRACTION

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
2.41	49.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.255	α = 90
b = 116.592	β = 90
c = 148.76	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		2023-12-02		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	1.74	91.86	99.9	0.164	0.171	0.046	0.997	8.7	13.6		73310

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	1.74	1.78		98.5	6.349	6.626	1.88	0.325		12.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5K5M	1.74	91.77	68107	3689	97.82	0.2055	0.2037	0.2684	0.2393	0.2877	RANDOM	59.498

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]
-3.74			0.57		3.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.372
r_dihedral_angle_4_deg	17.149
r_dihedral_angle_3_deg	15.332
r_dihedral_angle_1_deg	6.318
r_mcangle_it	5.323
r_mcbond_other	3.048
r_mcbond_it	3.028
r_angle_refined_deg	1.443
r_angle_other_deg	1.241
r_chiral_restr	0.068

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.372
r_dihedral_angle_4_deg	17.149
r_dihedral_angle_3_deg	15.332
r_dihedral_angle_1_deg	6.318
r_mcangle_it	5.323
r_mcbond_other	3.048
r_mcbond_it	3.028
r_angle_refined_deg	1.443
r_angle_other_deg	1.241
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4651
Nucleic Acid Atoms
Solvent Atoms	364
Heterogen Atoms	76

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.