4EQK | pdb_00004eqk

Crystal structure of the cap-binding domain of polymerase basic protein 2 from influenza virus A/Hong Kong/1/68 (h3n2) with bound m7GTP

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	8	293	0.2M lithium nitrate, 0.1M Tris-HCl pH 8.0, 18% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.379	α = 90
b = 70.151	β = 90
c = 93.941	γ = 90

Symmetry
Space Group	I 2 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	CCD	MARMOSAIC 225 mm CCD		2010-05-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9795	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.95	30	91.7		11.9	12525	12525

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	1.95	28.26	12491	11879	612	91.48	0.2276	0.18656	0.18349	0.18	0.24627	0.24	RANDOM	43.353

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]
-0.23			0.18		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.079
r_dihedral_angle_3_deg	17.847
r_dihedral_angle_4_deg	16.735
r_sphericity_free	7.952
r_dihedral_angle_1_deg	6.8
r_scangle_it	6.111
r_sphericity_bonded	4.376
r_scbond_it	3.973
r_mcangle_it	2.703
r_rigid_bond_restr	2.588
r_angle_refined_deg	2.258
r_mcbond_it	1.664
r_chiral_restr	0.161
r_bond_refined_d	0.022
r_gen_planes_refined	0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1293
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	37

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling