2YI9

Structure of the RNA polymerase VP1 from Infectious Pancreatic Necrosis Virus in complex with magnesium

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PGG	PDB ENTRY 2PGG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.65	CRYSTALS WERE GROWN IN SITTING DROPS CONTAINING 200 NL PROTEIN (5.8-6.8 MG/ML) AND 100 NL RESERVOIR SOLUTION (20-18% W/V PEG 3350, 0.10-0.09 M BIS-TRIS PROPANE PH 7.5, 0.2-0.18 M SODIUM CITRATE) EQUILIBRATED AGAINST 95 UL RESERVOIRS AT 20.5 DEGREES CELSIUS. CRYSTALS WERE SOAKED BY DILUTING THE MOTHER-LIQUOR WITH APPROX. 0.5 UL 20% W/V PEG 3350, 0.1 M BIS-TRIS PROPANE PH 8.25 AND 20% V/V GLYCEROL, TRANSFERRING THE CRYSTALS TO A FRESH DROP CONTAINING 20% W/V PEG 3350, 0.1 M BIS-TRIS PROPANE PH 8.25, 20% V/V GLYCEROL, 50 MM MGCL2 AND 10 UM GTP, AND INCUBATING FOR 10 MIN.

Crystal Properties
Matthews coefficient	Solvent content
3.36	63.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.048	α = 90
b = 183.874	β = 90
c = 244.521	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	CCD	ADSC CCD		2009-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

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	2.2	101.81	100	0.17	10.6	7.3		304685		-3	28.03

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	2.2	2.26	100		0.75	2.7	7.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2PGG	2.2	32.21	304439	3069	100	0.1605	0.1603	0.1812	RANDOM	27.7

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]
1.3797			-1.5091		0.1295

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	15.17
t_omega_torsion	3.2
t_angle_deg	0.98
t_bond_d	0.011
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	30143
Nucleic Acid Atoms
Solvent Atoms	2989
Heterogen Atoms	16

Software

Software
Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing