Experiment: 9DAP

Human norovirus GII.3 protease in complex with rupintrivir

X-RAY DIFFRACTION

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, HANGING DROP	5.5	298	0.3 M Sodium Formate, 0.1 M Sodium Citrate Tribasic:HCl, 22.5 % (v/v) PurePEGs Cocktail

Crystal Properties
Matthews coefficient	Solvent content
3.09	60.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.329	α = 90
b = 97.329	β = 90
c = 43.77	γ = 120

Symmetry
Space Group	P 32 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	298	PIXEL	DECTRIS PILATUS3 S 2M		2023-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1	ALS	8.2.2

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	2.71	48.66	99.78	0.04753	0.06721	0.04753	0.997	9.86	1.1		6699			50.06

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	2.71	3.41	99.67		0.963	3.85	1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.71	48.66	1.35	6685	318	99.79	0.1889	0.1864	0.1864	0.2403	0.2402	51.27

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.5643
f_angle_d	1.0065
f_chiral_restr	0.0531
f_plane_restr	0.0076
f_bond_d	0.0064

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1217
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	43

Software

Software
Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
pointless	data scaling
MOLREP	phasing