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Structure of Influenza A H5N1 PB2 cap-binding domain with bound cap analogue (compound 11)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VQZ PDB ENTRY 2VQZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.3 0.2 M AMMONIUM IODIDE, PH 6.3, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.09 41.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.17 α = 90 b = 31.13 β = 118.27 c = 98.79 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2009-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 50 98.8 0.09 8.6 2.95 24866
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.99 98.5 0.41 2.6 2.52
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 PDB ENTRY 2VQZ 1.9 45.41 23598 1268 98.97 0.21466 0.21141 0.2164 0.2745 0.274 RANDOM 26.847
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] -0.1 -0.02 -0.19 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.472 r_dihedral_angle_4_deg 15.781 r_dihedral_angle_3_deg 14.831 r_dihedral_angle_1_deg 5.969 r_angle_refined_deg 1.615 r_angle_other_deg 1.052 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.472 r_dihedral_angle_4_deg 15.781 r_dihedral_angle_3_deg 14.831 r_dihedral_angle_1_deg 5.969 r_angle_refined_deg 1.615 r_angle_other_deg 1.052 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.004 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 Atoms Number Protein Atoms 2580 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing