3KHW

Crystal structure of the large c-terminal domain of polymerase basic protein 2 from influenza virus a/mexico/indre4487/2009(h1n1)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29320% PEG 3350, 200MM AMMONIUM CITRATE, PROTEIN CONCENTRATION 24.4 MG/ML, VAPOR DIFFUSIONI, SITTING DROP, TEMPERATURE 293K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.1642.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.859α = 90
b = 68.185β = 90
c = 107.352γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+MIRRORS2009-10-27MSINGLE 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
12.15099.60.07811.56.723727
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)
12.12.1496.60.1945.1

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 REPLACEMENTTHROUGHOUT3KC62.1502367012180.1970.1940.238RANDOM7.83
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]
0.91-0.69-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.73
r_dihedral_angle_4_deg19.266
r_dihedral_angle_3_deg14.15
r_dihedral_angle_1_deg6.033
r_scangle_it2.531
r_scbond_it1.619
r_angle_refined_deg1.316
r_mcangle_it0.985
r_angle_other_deg0.883
r_mcbond_it0.552
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.73
r_dihedral_angle_4_deg19.266
r_dihedral_angle_3_deg14.15
r_dihedral_angle_1_deg6.033
r_scangle_it2.531
r_scbond_it1.619
r_angle_refined_deg1.316
r_mcangle_it0.985
r_angle_other_deg0.883
r_mcbond_it0.552
r_mcbond_other0.136
r_chiral_restr0.076
r_bond_refined_d0.012
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 Atoms3095
Nucleic Acid Atoms
Solvent Atoms234
Heterogen Atoms6

Software

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