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Crystal structure of the cap-binding domain of the PB2 subunit of influenza A/H5N1 polymerase bound to an azaindazole inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CB7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M di NaH phosphate and 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.16 43.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.49 α = 90 b = 62.49 β = 90 c = 69.97 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2013-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0615 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1 54.12 94 0.065 0.996 12.61 4.46 74557
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1 1.06 70.8 0.508 0.846 1.46 2.04
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4CB7 1 54.12 74557 3907 93.98 0.14063 0.13945 0.1392 0.16376 0.164 RANDOM 19.689
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] 0.27 0.14 0.27 -0.88
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 31.36 r_dihedral_angle_2_deg 27.719 r_dihedral_angle_4_deg 13.613 r_dihedral_angle_3_deg 12.954 r_sphericity_bonded 9.502 r_dihedral_angle_1_deg 5.839 r_long_range_B_other 3.283 r_long_range_B_refined 3.281 r_scangle_other 2.728 r_scbond_it 2.297
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 31.36 r_dihedral_angle_2_deg 27.719 r_dihedral_angle_4_deg 13.613 r_dihedral_angle_3_deg 12.954 r_sphericity_bonded 9.502 r_dihedral_angle_1_deg 5.839 r_long_range_B_other 3.283 r_long_range_B_refined 3.281 r_scangle_other 2.728 r_scbond_it 2.297 r_scbond_other 2.297 r_mcangle_it 2.111 r_mcangle_other 2.11 r_rigid_bond_restr 1.675 r_angle_refined_deg 1.587 r_mcbond_it 1.575 r_mcbond_other 1.553 r_angle_other_deg 1.101 r_chiral_restr 0.098 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1226 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing