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Three viral endonucleases bound to the same inhibitor (9-hydroxy-3,4-dihydro-2H-pyrazino[1,2-c]pyrimidine-1,8-dione derivative). (1b) Influenza virus A/pH1N1 polymerase PA subunit endonuclease with manganese ions.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AWK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 288 5 mM MnCl2
0.1 M Hepes sodium pH7.5
0.7 M Tri-sodium citrate dihydrate
Cryo: 20 % glycerol
Crystal Properties Matthews coefficient Solvent content 2.23 44.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.82 α = 90 b = 74.22 β = 90 c = 100.97 γ = 90
Symmetry Space Group P 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 MAR CCD 300 mm 2012-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 50 99.8 0.082 0.095 0.998 11.44 3.91 52701 27.74
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 99.5 0.697 0.743 0.743 1.91 3.87
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 47.49 1.18 52699 2654 99.8 0.1996 0.1978 0.2013 0.2336 0.2335 33.72
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.7325 f_angle_d 0.5738 f_chiral_restr 0.0409 f_plane_restr 0.0041 f_bond_d 0.0028
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2978 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 120
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing