4NCE | pdb_00004nce

Influenza polymerase basic protein 2 (PB2) bound to 7-methyl-GTP

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.7	298	0.7 uL of protein solution (9.7 mg/mL protein, 50 mM Tris buffer pH 8, 200 mM sodium chloride, 2 mM dithiothreitol, 5 mM m7GTP) was mixed with 0.35 uL Hampton Research Silver Bullet screening reagent #36. This mixture was combined with 0.35 uL of well solution (approximately 1.3 M sodium formate, 100 mM sodium citrate buffer pH 4.6, 5 mM dithiothreitol) and suspended over 1 mL of well solution, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.44	α = 90
b = 81.44	β = 90
c = 54.56	γ = 120

Symmetry
Space Group	P 65

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 315		2008-08-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.0	ALS	5.0.2

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	2.3	29.62	100	0.134	8.3	6.45	9272	9272	1	1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2VQZ	2.3	29.62	9272	8830	442	99.9	0.19625	0.19625	0.1946	0.2	0.22929	0.24	RANDOM	25.577

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]
0.85	0.42		0.85		-1.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.349
r_dihedral_angle_4_deg	21.365
r_dihedral_angle_3_deg	18.258
r_dihedral_angle_1_deg	6.455
r_scangle_it	2.62
r_scbond_it	1.596
r_angle_refined_deg	1.386
r_mcangle_it	0.893
r_mcbond_it	0.444
r_chiral_restr	0.104
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1290
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms	81

Software

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