3L56

Crystal structure of the large c-terminal domain of polymerase basic protein 2 from influenza virus a/viet nam/1203/2004 (h5n1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KC6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529320% PEG 3350, 200MM NACL, 100MM TRIS PH 8.5, PROTEIN CONCENTRATION 24.4 MG/ML, VAPOR DIFFUSIONI, SITTING DROP, TEMPERATURE 293K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
1.9235.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.042α = 90
b = 57.007β = 102.4
c = 83.081γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSATURN 944++MIRRORS2009-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54178

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
12.381.1498.10.029543.516536
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)
12.32.34820.0462.2

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3KC62.350165268400.180.1760.237RANDOM12.98
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]
0.33-0.46-0.26-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.474
r_dihedral_angle_4_deg20.268
r_dihedral_angle_3_deg14.815
r_dihedral_angle_1_deg6.109
r_scangle_it3.142
r_scbond_it1.966
r_angle_refined_deg1.377
r_mcangle_it1.373
r_angle_other_deg0.892
r_mcbond_it0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.474
r_dihedral_angle_4_deg20.268
r_dihedral_angle_3_deg14.815
r_dihedral_angle_1_deg6.109
r_scangle_it3.142
r_scbond_it1.966
r_angle_refined_deg1.377
r_mcangle_it1.373
r_angle_other_deg0.892
r_mcbond_it0.73
r_mcbond_other0.138
r_chiral_restr0.074
r_bond_refined_d0.014
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3100
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms

Software

Software
Software NamePurpose
StructureStudiodata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling