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18mer DNA mimic Foldamer with an Aliphatic linker in complex with Sac7d V26A/M29A protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8CMN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 9 % PEG 400, 0.1 M MES pH 6.0
Crystal Properties Matthews coefficient Solvent content 5.74 78.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.92 α = 90 b = 70.92 β = 90 c = 119.29 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 EIGER X 16M 2023-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
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 3.21 30.71 99.54 1 23.56 37.1 3226 115.53
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 3.21 3.32 100 0.952 3.51 39.9
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 3.21 30.71 1.37 3220 322 99.78 0.326 0.3249 0.3246 0.3345 0.3358 129.42
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 13.7308 f_angle_d 4.123 f_chiral_restr 0.2804 f_bond_d 0.0256 f_plane_restr 0.0254
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 474 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 346
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing