4X2W | pdb_00004x2w

Crystal structure of the Murine Norovirus NS6 protease (inactive C139A mutant) with a C-terminal extension to include residues P1 prime - P2 prime of NS7

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ASH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291.15	15% (v/v) PEG 3350, 0.1 M glycine, 0.1 M Na-citrate pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.93	57.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.94	α = 90
b = 135.94	β = 90
c = 82.38	γ = 120

Symmetry
Space Group	P 61 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	100	PIXEL	DECTRIS PILATUS 6M-F		2013-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	1.000	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.7	117.85	99.8	0.085	10.9	5.7		8555

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	3.1	3.31	99.6		0.915	2.1	6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4ASH	2.7	117.85	8555	469	74.39	0.256	0.2536	0.25	0.3025	0.29	Random selection	87.171

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]
0.99	0.49		0.99		-3.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.317
r_dihedral_angle_4_deg	20.35
r_dihedral_angle_3_deg	15.731
r_dihedral_angle_1_deg	8.67
r_mcangle_it	2.166
r_angle_refined_deg	1.608
r_mcbond_it	1.178
r_mcbond_other	1.178
r_angle_other_deg	1.129
r_chiral_restr	0.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.317
r_dihedral_angle_4_deg	20.35
r_dihedral_angle_3_deg	15.731
r_dihedral_angle_1_deg	8.67
r_mcangle_it	2.166
r_angle_refined_deg	1.608
r_mcbond_it	1.178
r_mcbond_other	1.178
r_angle_other_deg	1.129
r_chiral_restr	0.082
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2562
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
MOSFLM	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.