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Structure of Influenza A H5N1 PB2 cap-binding domain with bound m7GTP
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 4.6 0.1M SODIUM ACETATE PH 4.6, 2M NACL
Crystal Properties Matthews coefficient Solvent content 2.88 57.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.48 α = 90 b = 82.48 β = 90 c = 55.24 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 CCD MARMOSAIC 225 mm CCD 2009-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 1.6 50 99.3 0.08 10.62 3.72 28140
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 1.6 1.66 99.1 0.58 2.52 3.65
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 1.6 43.35 26753 1387 99.28 0.12798 0.12585 0.1418 0.1699 0.1764 RANDOM 17.205
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] 0.08 0.08 0.08 -0.27
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 29.999 r_dihedral_angle_2_deg 28.448 r_dihedral_angle_4_deg 15.736 r_dihedral_angle_3_deg 12.17 r_sphericity_bonded 8.197 r_dihedral_angle_1_deg 6.187 r_rigid_bond_restr 2.416 r_angle_refined_deg 1.538 r_angle_other_deg 0.759 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 29.999 r_dihedral_angle_2_deg 28.448 r_dihedral_angle_4_deg 15.736 r_dihedral_angle_3_deg 12.17 r_sphericity_bonded 8.197 r_dihedral_angle_1_deg 6.187 r_rigid_bond_restr 2.416 r_angle_refined_deg 1.538 r_angle_other_deg 0.759 r_chiral_restr 0.091 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1285 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing