22ZV | pdb_000022zv

norovirus GII23 P domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3R6J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	10% (v/v) PEG 200, 0.1 M BIS-TRIS propane (pH 9.0), and 18% (w/v) PEG 8,000

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.832	α = 90
b = 107.313	β = 90
c = 220.661	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS3 S 6M		2018-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.9792	SSRF	BL19U1

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	50	100	0.997	13.4	9.8		98555

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	2.03			0.872

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2	47.761	98410	4880	99.881	0.185	0.1824	0.1912	0.228	0.2353	25.828

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]
-0.613			-1.757		2.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.913
r_dihedral_angle_3_deg	13.416
r_dihedral_angle_1_deg	7.084
r_lrange_it	6.716
r_dihedral_angle_2_deg	6.706
r_lrange_other	6.655
r_scangle_it	4.836
r_scangle_other	4.836
r_mcangle_it	3.509
r_mcangle_other	3.509
r_scbond_it	3.134
r_scbond_other	3.134
r_mcbond_it	2.356
r_mcbond_other	2.352
r_angle_refined_deg	1.397
r_angle_other_deg	0.47
r_symmetry_nbd_refined	0.271
r_nbd_other	0.212
r_symmetry_nbd_other	0.204
r_nbd_refined	0.194
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.162
r_symmetry_xyhbond_nbd_refined	0.161
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.065
r_symmetry_xyhbond_nbd_other	0.053
r_xyhbond_nbd_other	0.049
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9728
Nucleic Acid Atoms
Solvent Atoms	838
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing