9T3J | pdb_00009t3j

Protease from Norovirus Sydney GII.4 strain with crystallization epitope mutation H50Y

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6NIR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293.15	Ligand-friendly screen, condition F02 20% PEG3350 10% ethylene glycol 0.1M bis-tris-propane pH 6.5 0.2M sodium bromide

Crystal Properties
Matthews coefficient	Solvent content
3.84	67.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.895	α = 90
b = 128.895	β = 90
c = 118.126	γ = 120

Symmetry
Space Group	P 61

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 X 16M		2023-12-09	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	2.41	81.132	100	0.999	10.3	42.5		43061

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	2.41	2.45			0.413

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	2.411	81.132	39586	1740	92.026	0.211	0.2093	0.2092	0.252	0.2518	RANDOM	89.056

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]
1.569	0.784		1.569		-5.089

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	20.871
r_lrange_other	20.871
r_dihedral_angle_3_deg	19.204
r_scangle_it	17.791
r_scangle_other	17.788
r_mcangle_it	17.047
r_mcangle_other	17.045
r_dihedral_angle_6_deg	15.53
r_scbond_it	13.465
r_scbond_other	13.464
r_mcbond_it	12.699
r_mcbond_other	12.686
r_dihedral_angle_2_deg	12.336
r_dihedral_angle_1_deg	9.038
r_angle_refined_deg	2.463
r_angle_other_deg	0.946
r_symmetry_nbd_refined	0.192
r_nbd_refined	0.191
r_symmetry_nbd_other	0.173
r_nbtor_refined	0.171
r_nbd_other	0.169
r_ncsr_local_group_4	0.159
r_ncsr_local_group_3	0.157
r_ncsr_local_group_5	0.157
r_symmetry_xyhbond_nbd_refined	0.148
r_ncsr_local_group_6	0.148
r_ncsr_local_group_2	0.144
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.122
r_ncsr_local_group_1	0.106
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5126
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms

Software

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