22ZW | pdb_000022zw

norovirus GII24 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	0.1M sodium acetate trihydrate (pH 4.0) with 10% (w/v) PEG4,000

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.629	α = 90
b = 80.304	β = 90
c = 134.287	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 EIGER2 S 9M		2018-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.97918	SSRF	BL10U2

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	2.35	38.278	99.7	0.64	9.9	10		33685

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	2.35	2.411			0.64

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	2.35	38.278	33685	1662	99.372	0.234	0.2315	0.2416	0.286	0.2882	39.572

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]
-3.021			-1.3		4.322

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.422
r_dihedral_angle_6_deg	14.955
r_lrange_it	7.822
r_lrange_other	7.791
r_dihedral_angle_1_deg	7.654
r_dihedral_angle_2_deg	6.957
r_scangle_it	5.466
r_scangle_other	5.465
r_mcangle_it	4.93
r_mcangle_other	4.929
r_scbond_it	3.426
r_scbond_other	3.425
r_mcbond_it	3.174
r_mcbond_other	3.174
r_angle_refined_deg	1.325
r_angle_other_deg	0.46
r_symmetry_nbd_refined	0.237
r_nbd_other	0.235
r_nbd_refined	0.221
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.166
r_symmetry_xyhbond_nbd_refined	0.107
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.06
r_chiral_restr_other	0.031
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_symmetry_xyhbond_nbd_other	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4859
Nucleic Acid Atoms
Solvent Atoms	214
Heterogen Atoms	2

Software

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