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SARM1 TIR domain in complex with compound 28-ADPR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8D0F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Bis-Tris propane pH 6.5, 14-18% (w/v) PEG 3350 and 0.30-0.45 M potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.26 45.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.146 α = 90 b = 78.014 β = 90 c = 115.9 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 PIXEL DECTRIS EIGER2 S 16M 2023-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.885603 ESRF ID23-1
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 1.988 64.718 90.5 0.24 0.983 5.6 6.2 14405
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 1.99 2.11 0.718 0.724
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 1.988 64.718 13630 768 66.97 0.19953 0.19727 0.2035 0.24058 0.2407 RANDOM 16.296
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] 0.09 -0.41 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.874 r_dihedral_angle_2_deg 7.683 r_dihedral_angle_1_deg 7.185 r_long_range_B_refined 4.886 r_long_range_B_other 4.882 r_scangle_other 3.523 r_mcangle_it 2.389 r_mcangle_other 2.389 r_scbond_it 2.101 r_scbond_other 2.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.874 r_dihedral_angle_2_deg 7.683 r_dihedral_angle_1_deg 7.185 r_long_range_B_refined 4.886 r_long_range_B_other 4.882 r_scangle_other 3.523 r_mcangle_it 2.389 r_mcangle_other 2.389 r_scbond_it 2.101 r_scbond_other 2.1 r_angle_refined_deg 1.699 r_mcbond_it 1.403 r_mcbond_other 1.402 r_angle_other_deg 0.567 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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 2244 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement STARANISO data scaling XDS data reduction PHASER phasing