2FYQ | pdb_00002fyq

Crystal Structure of the Norwalk Virus Protease

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5	298	0.1M lithium sulfate, 0.1M bis-tris, 0.1M EDTA, 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 5.50

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.833	α = 90
b = 121.833	β = 90
c = 51.369	γ = 120

Symmetry
Space Group	P 65 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	ADSC QUANTUM 4			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9794	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.5	31.5	99.1				36055

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.5	1.55			0.457	4.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1.5	105.41	36046	36046	1800	99	0.185	0.18	0.211	0.21	17.31

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]
-0.06	-0.03		-0.06		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.522
r_dihedral_angle_4_deg	17.037
r_dihedral_angle_3_deg	11.219
r_dihedral_angle_1_deg	6.485
r_sphericity_free	3.076
r_scangle_it	2.794
r_sphericity_bonded	2.148
r_scbond_it	2.116
r_rigid_bond_restr	1.694
r_mcangle_it	1.494
r_angle_refined_deg	1.207
r_mcbond_it	0.955
r_symmetry_vdw_refined	0.437
r_nbtor_refined	0.305
r_symmetry_hbond_refined	0.276
r_nbd_refined	0.215
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.083
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1271
Nucleic Acid Atoms
Solvent Atoms	293
Heterogen Atoms	7

Software

Software
Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction