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Influenza B/Memphis/13/03 endonuclease with bound inhibitor, baloxavir acid (BXA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FML PDB:5FML
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 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 0.2 M NaCl, 0.1 M Na(CH3)2AsO2 pH 6.5, 2 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.39 48.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.82 α = 90 b = 59.82 β = 90 c = 125.89 γ = 90
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 PILATUS 6M 2017-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.254 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 59.86 91.8 0.064 0.998 13.6 3.6 37506 20.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 93.7 0.471 0.862 2.6 3.4
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 MOLECULAR REPLACEMENT THROUGHOUT PDB:5FML 1.8 59.86 35748 1758 91.78 0.18494 0.18344 0.1928 0.21507 0.2225 RANDOM 24.202
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] 0.62 0.62 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.744 r_dihedral_angle_4_deg 17.357 r_dihedral_angle_3_deg 13.492 r_dihedral_angle_1_deg 5.167 r_long_range_B_refined 4.545 r_long_range_B_other 4.501 r_scangle_other 3.322 r_mcangle_other 2.596 r_mcangle_it 2.595 r_scbond_it 2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.744 r_dihedral_angle_4_deg 17.357 r_dihedral_angle_3_deg 13.492 r_dihedral_angle_1_deg 5.167 r_long_range_B_refined 4.545 r_long_range_B_other 4.501 r_scangle_other 3.322 r_mcangle_other 2.596 r_mcangle_it 2.595 r_scbond_it 2.08 r_scbond_other 2.079 r_mcbond_it 1.625 r_mcbond_other 1.617 r_angle_refined_deg 1.437 r_angle_other_deg 0.907 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2942 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing