4EQK

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

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VQZPDB ENTRY 2VQZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82930.2M lithium nitrate, 0.1M Tris-HCl pH 8.0, 18% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3647.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.379α = 90
b = 70.151β = 90
c = 93.941γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-05-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.9795SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.953091.711.91252512525

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2VQZ1.9528.26124911187961291.480.22760.186560.183490.24627RANDOM43.353
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]
-0.230.180.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.079
r_dihedral_angle_3_deg17.847
r_dihedral_angle_4_deg16.735
r_sphericity_free7.952
r_dihedral_angle_1_deg6.8
r_scangle_it6.111
r_sphericity_bonded4.376
r_scbond_it3.973
r_mcangle_it2.703
r_rigid_bond_restr2.588
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.079
r_dihedral_angle_3_deg17.847
r_dihedral_angle_4_deg16.735
r_sphericity_free7.952
r_dihedral_angle_1_deg6.8
r_scangle_it6.111
r_sphericity_bonded4.376
r_scbond_it3.973
r_mcangle_it2.703
r_rigid_bond_restr2.588
r_angle_refined_deg2.258
r_mcbond_it1.664
r_chiral_restr0.161
r_bond_refined_d0.022
r_gen_planes_refined0.011
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 AtomsNumber
Protein Atoms1293
Nucleic Acid Atoms
Solvent Atoms79
Heterogen Atoms37

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling