4CHE

Crystal structure of the putative cap-binding domain of the PB2 subunit of Thogoto virus polymerase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16293THE PROTEIN WAS CONCENTRATED TO 9 MG/ML IN A BUFFER CONTAINING 20 MM TRIS PH 7.0, 200 MM NACL AND 5 MM BETA-MERCAPTOETHANOL. THE BEST-DIFFRACTING CRYSTALS GREW WITHIN 2 DAYS AT 20 C IN A SOLUTION CONTAINING 100 MM BIS-TRIS PH 6.0, 100 MM MGCL2 AND 22 % PEG3350.
Crystal Properties
Matthews coefficientSolvent content
3.160.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.62α = 90
b = 109.62β = 90
c = 39.06γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.85099.70.0616.55.221746
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8599.60.642.43.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUTNONE1.877.6220631111599.670.172680.171610.19215RANDOM25.115
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]
-0.65-0.651.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.395
r_dihedral_angle_4_deg16.232
r_dihedral_angle_3_deg10.836
r_dihedral_angle_1_deg5.861
r_angle_refined_deg1.204
r_angle_other_deg0.803
r_chiral_restr0.081
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.395
r_dihedral_angle_4_deg16.232
r_dihedral_angle_3_deg10.836
r_dihedral_angle_1_deg5.861
r_angle_refined_deg1.204
r_angle_other_deg0.803
r_chiral_restr0.081
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1305
Nucleic Acid Atoms
Solvent Atoms188
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing