3R2V | pdb_00003r2v

Crystal structure of polymerase basic protein 2 E538-R753 from Influenza A virus A/Yokohama/2017/03 H3N2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VY6	PDB entry 2VY6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	289	InvaB.07055.c.D17 PD00118 at 24.51 mg/mL against 0.1 M MIB pH 6.0, 25% PEG 1500, 100 mM NaI, crystal tracking ID 220930b6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.81	α = 90
b = 106.54	β = 90
c = 33.49	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	ADSC QUANTUM 315r		2011-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.97946	ALS	5.0.1

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	1.3	50	97.6	0.04	21.66	5.4	47417	46293		-3	19.242

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	1.3	1.33	86.7		0.319	3.27	3.1	3441

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	SAD, MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2VY6	1.3	30	46148	2293	97.32	0.1816	0.1802	0.2	0.2094	0.19	RANDOM	17.4682

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]
0.18			-0.36		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.175
r_dihedral_angle_4_deg	15.564
r_dihedral_angle_3_deg	11.757
r_dihedral_angle_1_deg	5.293
r_scangle_it	3.812
r_scbond_it	2.592
r_mcangle_it	1.984
r_angle_refined_deg	1.278
r_mcbond_it	1.214
r_rigid_bond_restr	1.199

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.175
r_dihedral_angle_4_deg	15.564
r_dihedral_angle_3_deg	11.757
r_dihedral_angle_1_deg	5.293
r_scangle_it	3.812
r_scbond_it	2.592
r_mcangle_it	1.984
r_angle_refined_deg	1.278
r_mcbond_it	1.214
r_rigid_bond_restr	1.199
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1477
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	15

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
BOS	data collection
XDS	data reduction

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.