3KC6

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 3CW4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP10.52935% SBOG, 100MM CAPS PH 10.5, 1.2 M SODIUM PHOSPHATE, 0.2 M LITHIUM PHOSPHATE, 0.8 M POTASSIUM PHOSPHATE. PROTEIN CONCENTRATION 8.25 MG/ML, VAPOR DIFFUSIONI, SITTING DROP, TEMPERATURE 293K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.3146.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.084α = 90
b = 65.696β = 90
c = 96.855γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+MIRRORS2009-08-31MSINGLE 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
12.055098.70.0799.15.613728
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)
12.052.0988.50.3284

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 REPLACEMENTTHROUGHOUT3CW42.0550136826840.2040.2020.245RANDOM9.38
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]
0.29-1.010.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.82
r_dihedral_angle_4_deg20.226
r_dihedral_angle_3_deg13.746
r_dihedral_angle_1_deg5.77
r_scangle_it2.396
r_scbond_it1.453
r_angle_refined_deg1.187
r_mcangle_it1.054
r_angle_other_deg0.834
r_mcbond_it0.582
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.82
r_dihedral_angle_4_deg20.226
r_dihedral_angle_3_deg13.746
r_dihedral_angle_1_deg5.77
r_scangle_it2.396
r_scbond_it1.453
r_angle_refined_deg1.187
r_mcangle_it1.054
r_angle_other_deg0.834
r_mcbond_it0.582
r_mcbond_other0.106
r_chiral_restr0.064
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 Atoms1503
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms12

Software

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