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Crystal structure of polymerase basic protein 2 E538-R753 from Influenza A virus A/Yokohama/2017/03 H3N2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VY6 PDB entry 2VY6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 289 InvaB.07055.c.D17 PD00118 at 24.51 mg/mL against 0.1 M MIB pH 6.0, 25% PEG 1500, 100 mM NaI, crystal tracking ID 220930b6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.94 36.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.81 α = 90 b = 106.54 β = 90 c = 33.49 γ = 90
Symmetry Space Group P 21 21 2
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 2011-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97946 ALS 5.0.1
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 1.3 50 97.6 0.04 21.66 5.4 47417 46293 -3 19.242
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 1.3 1.33 86.7 0.319 3.27 3.1 3441
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 SAD, MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2VY6 1.3 30 46148 2293 97.32 0.1816 0.1802 0.1992 0.2094 0.1925 RANDOM 17.4682
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] 0.18 -0.36 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.175 r_dihedral_angle_4_deg 15.564 r_dihedral_angle_3_deg 11.757 r_dihedral_angle_1_deg 5.293 r_scangle_it 3.812 r_scbond_it 2.592 r_mcangle_it 1.984 r_angle_refined_deg 1.278 r_mcbond_it 1.214 r_rigid_bond_restr 1.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.175 r_dihedral_angle_4_deg 15.564 r_dihedral_angle_3_deg 11.757 r_dihedral_angle_1_deg 5.293 r_scangle_it 3.812 r_scbond_it 2.592 r_mcangle_it 1.984 r_angle_refined_deg 1.278 r_mcbond_it 1.214 r_rigid_bond_restr 1.199 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1477 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 15
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction BOS data collection XDS data reduction