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Influenza A/California/07/2009(H1N1) endonuclease with I38T mutation in complex with orientin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YA5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291.15 MDP, PEG 1000, PEG 3350, Sodium HEPES, MOPS (acid), Magnesium chloride, Calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.33 47.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.967 α = 90 b = 73.967 β = 90 c = 127.575 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 300K 2021-01-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54187
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 2.2 45.24 99.2 0.088 0.095 0.998 15.96 6.793 10985 41.708
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 2.26 98.1 1.166 1.325 0.386 1.21 4.187
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 6YA5 2.2 45.24 10437 549 99.17 0.1963 0.1927 0.2014 0.2641 0.2776 RANDOM 42.106
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] -0.28 -0.14 -0.28 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.911 r_dihedral_angle_4_deg 15.129 r_dihedral_angle_3_deg 15.029 r_dihedral_angle_1_deg 6.756 r_angle_refined_deg 1.478 r_angle_other_deg 1.276 r_chiral_restr 0.06 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.911 r_dihedral_angle_4_deg 15.129 r_dihedral_angle_3_deg 15.029 r_dihedral_angle_1_deg 6.756 r_angle_refined_deg 1.478 r_angle_other_deg 1.276 r_chiral_restr 0.06 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1429 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MOLREP phasing