9T4P | pdb_00009t4p

Dengue 2 Virus NS2B-NS3 protease fusion protein with crystal epitope mutation K174Q

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4M9M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293.15	LFS Eco well C09 0.1M HEPES pH 7, 0.2M Lithium chloride, 20% w/v PEG 6000, 10% v/v Ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.486	α = 90
b = 45.2	β = 109.108
c = 40.46	γ = 90

Symmetry
Space Group	C 1 2 1

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 EIGER X 16M		2024-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976269	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.95	42.15	99.86	0.999	10	6.8		15533

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	1.98			0.357

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.95	42.148	15533	800	99.852	0.229	0.2257	0.2259	0.2939	0.294	RANDOM	53.484

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]
-0.249		-0.097	0.131		0.149

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.798
r_dihedral_angle_2_deg	17.341
r_dihedral_angle_6_deg	17.111
r_lrange_other	13.604
r_lrange_it	13.6
r_scangle_it	11.573
r_scangle_other	11.568
r_dihedral_angle_1_deg	9.404
r_mcangle_it	8.596
r_mcangle_other	8.593
r_scbond_it	8.489
r_scbond_other	8.484
r_mcbond_it	6.575
r_mcbond_other	6.56
r_angle_refined_deg	2.72
r_angle_other_deg	1.22
r_symmetry_xyhbond_nbd_refined	0.203
r_nbd_refined	0.179
r_xyhbond_nbd_refined	0.179
r_nbtor_refined	0.156
r_symmetry_nbd_other	0.144
r_nbd_other	0.141
r_chiral_restr	0.138
r_symmetry_nbd_refined	0.086
r_symmetry_nbtor_other	0.078
r_symmetry_xyhbond_nbd_other	0.033
r_bond_refined_d	0.014
r_gen_planes_refined	0.014
r_bond_other_d	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1483
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing