4AWM

Influenza strain pH1N1 2009 polymerase subunit PA endonuclease in complex with (-)-epigallocatechin gallate from green tea


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2W69PDB ENTRY 2W69

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1710% PEG 3350, 0.1 M NACL, 0.1 M HEPES PH 7
Crystal Properties
Matthews coefficientSolvent content
2.6653.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.94α = 90
b = 99.94β = 90
c = 82.73γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-04-12MSINGLE 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
12.65098.30.1512.110.57797
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)
12.62.796.70.843.1410.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2W692.642.78743436398.480.225550.22310.2784RANDOM38.275
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]
9.639.63-19.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.265
r_dihedral_angle_4_deg19.544
r_dihedral_angle_3_deg16.294
r_dihedral_angle_1_deg4.975
r_angle_refined_deg1.181
r_angle_other_deg0.794
r_chiral_restr0.059
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.265
r_dihedral_angle_4_deg19.544
r_dihedral_angle_3_deg16.294
r_dihedral_angle_1_deg4.975
r_angle_refined_deg1.181
r_angle_other_deg0.794
r_chiral_restr0.059
r_bond_refined_d0.008
r_gen_planes_refined0.004
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 Atoms1481
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing