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Influenza A/California/07/2009(H1N1) endonuclease in complex with purpurogallin-like compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NUG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291.15 MDP, PEG 1000, PEG 3350, Sodium HEPES, MOPS (acid), Magnesium chloride, Calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.31 46.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.95 α = 90 b = 73.95 β = 90 c = 126.61 γ = 120
Symmetry Space Group P 64 2 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 PIXEL DECTRIS PILATUS 6M 2023-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 1.93 50 99 0.098 0.10099999999999999 1 19.85 17.2 28879
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 1.93 2.05 2.167 2.331 0.29600000000000004
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2 45.02 13683 721 99.45 0.21831 0.21587 0.2252 0.26548 0.2686 RANDOM 44.982
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] -0.46 -0.23 -0.46 1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.985 r_dihedral_angle_2_deg 8.24 r_long_range_B_refined 7.889 r_long_range_B_other 7.887 r_scangle_other 6.018 r_dihedral_angle_1_deg 5.852 r_mcangle_it 5.397 r_mcangle_other 5.394 r_scbond_it 4.114 r_scbond_other 4.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.985 r_dihedral_angle_2_deg 8.24 r_long_range_B_refined 7.889 r_long_range_B_other 7.887 r_scangle_other 6.018 r_dihedral_angle_1_deg 5.852 r_mcangle_it 5.397 r_mcangle_other 5.394 r_scbond_it 4.114 r_scbond_other 4.111 r_mcbond_it 3.995 r_mcbond_other 3.988 r_angle_refined_deg 1.271 r_angle_other_deg 0.443 r_chiral_restr 0.058 r_bond_refined_d 0.009 r_bond_other_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 1450 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction MOLREP phasing