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Crystal structure of the cap-binding domain of polymerase basic protein 2 from influenza virus A/Bar-headed Gs/Qinghai/15c/2005 (h5n1) with bound m7GTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VQZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 0.1M Ammonium sulfate, 0.01M Magnesium chloride, 0.05M MES pH5.6, 22% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.19 43.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.48 α = 90 b = 39.1 β = 102.38 c = 141.08 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 225 mm CCD 2010-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9795 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 14.91 99.1 63747 63747
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2VQZ 1.8 14.91 62212 59069 3153 99.71 0.20166 0.19724 0.1953 0.28495 0.282 RANDOM 32.436
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] -0.06 -0.01 0.16 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.686 r_dihedral_angle_3_deg 18.561 r_dihedral_angle_4_deg 18.01 r_sphericity_free 10.489 r_dihedral_angle_1_deg 6.941 r_sphericity_bonded 6.066 r_scangle_it 5.501 r_scbond_it 3.874 r_mcangle_it 2.748 r_rigid_bond_restr 2.487
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.686 r_dihedral_angle_3_deg 18.561 r_dihedral_angle_4_deg 18.01 r_sphericity_free 10.489 r_dihedral_angle_1_deg 6.941 r_sphericity_bonded 6.066 r_scangle_it 5.501 r_scbond_it 3.874 r_mcangle_it 2.748 r_rigid_bond_restr 2.487 r_angle_refined_deg 2.184 r_mcbond_it 1.831 r_chiral_restr 0.154 r_bond_refined_d 0.024 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5148 Nucleic Acid Atoms Solvent Atoms 578 Heterogen Atoms 152
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling