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Crystal structure of SNAr1.3 (K39A) in complex with 2,4-dinitroiodobenzene
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7O1D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 M sodium citrate tribasic dihydrate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.1 60.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.364 α = 90 b = 70.364 β = 90 c = 119.519 γ = 120
Symmetry Space Group P 31 2 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 EIGER2 XE 16M 2024-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.71 54.29 100 1 13.8 20.1 37752 35.48
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.71 1.75 0.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.71 42.67 1.33 37485 1959 99.41 0.2058 0.2038 0.2044 0.243 0.2436 45.28
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 16.6252 f_angle_d 0.6222 f_chiral_restr 0.0455 f_bond_d 0.0058 f_plane_restr 0.0051
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1842 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing