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Middle domain of influenza A virus RNA-dependent polymerase PB2
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 VAPOR DIFFUSION, HANGING DROP 5.9 277 0.1M NaH2PO4, 0.1M KH2PO4, 0.1M MES (pH 5.9), 0.8M NaCl, 4% (v/v) 1-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.82 56.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.969 α = 90 b = 103.511 β = 90 c = 112.526 γ = 90
Symmetry Space Group I 21 21 21
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 210r 2012-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 2.42 31.42 93.5 0.045 45 7.1 16108
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 2.42 2.47 98.9 0.33 45.1 7.1 824
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 (All) 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 2.42 25.88 16108 15240 803 92.48 0.21828 0.21828 0.21545 0.2156 0.2711 0.2671 RANDOM 58
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] -1.46 1.14 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.313 r_dihedral_angle_4_deg 19.408 r_dihedral_angle_3_deg 18.68 r_dihedral_angle_1_deg 7.234 r_angle_refined_deg 1.787 r_angle_other_deg 0.906 r_chiral_restr 0.109 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.313 r_dihedral_angle_4_deg 19.408 r_dihedral_angle_3_deg 18.68 r_dihedral_angle_1_deg 7.234 r_angle_refined_deg 1.787 r_angle_other_deg 0.906 r_chiral_restr 0.109 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 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_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2582 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling