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Influenza B/Memphis/13/03 endonuclease with I38T mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FML
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Protein, at 15-17 mg/ml, was incubated with 10-fold molar excess of BXA for 30 min at RT, mixtures were centrifuged at RT for 5 minutes at 12000 g, and soluble fraction was used for crystallization trials (final protein concentration 8-10 mg/ml).
Mother liquor was
Crystal Properties Matthews coefficient Solvent content 2.29 46.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.98 α = 90 b = 61.45 β = 95.47 c = 92.63 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 PIXEL DECTRIS PILATUS3 2M 2017-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.8 50 91.3 0.055 0.996 7.55 1.7 39336
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 92.4 0.58 0.596 1.17 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5FML 1.8 46.104 1.37 37473 1863 94.92 0.1988 0.1968 0.2093 0.2361 0.2459
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 13.759 f_angle_d 1.043 f_chiral_restr 0.06 f_bond_d 0.011 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3235 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 3
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing