2PNL

Crystal structure of VP4 protease from infectious pancreatic necrosis virus (IPNV) in space group P1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	0.1M Tris-HCl pH 8.5, 35% PEG 4000, 0.4M LiSO4, 0.4M Guanidine-HCl , VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.703	α = 93.06
b = 69.262	β = 95.03
c = 191.388	γ = 97.56

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4	mirrors	2006-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C	0.9792	NSLS	X8C

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	2.21	182.57	97.5	0.082	20.7	3.9	103935	103935	2	2

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)
	2.21	2.29	91.5		0.28	4.5	3.4	9718

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.21	182.57	103935	103863	5185	98.27	0.2	0.194	0.19	0.267	RANDOM	24.932

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]
-0.08	-0.86	-0.65	1.66	-0.26	-1.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.474
r_dihedral_angle_4_deg	20.643
r_dihedral_angle_3_deg	17.978
r_dihedral_angle_1_deg	6.92
r_scangle_it	3.968
r_scbond_it	2.675
r_angle_refined_deg	1.754
r_mcangle_it	1.591
r_mcbond_it	1.083
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.474
r_dihedral_angle_4_deg	20.643
r_dihedral_angle_3_deg	17.978
r_dihedral_angle_1_deg	6.92
r_scangle_it	3.968
r_scbond_it	2.675
r_angle_refined_deg	1.754
r_mcangle_it	1.591
r_mcbond_it	1.083
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.257
r_nbd_refined	0.238
r_symmetry_hbond_refined	0.192
r_xyhbond_nbd_refined	0.185
r_chiral_restr	0.12
r_bond_refined_d	0.018
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15142
Nucleic Acid Atoms
Solvent Atoms	1216
Heterogen Atoms	68

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.