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Radiation damage study on a 16mer DNA segment, structure at 17.7 MGy dose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QT1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.6 292 2 microliter 1.5 mM DNA solution (5mM HEPES pH 6.6) plus 2 microliter 10 mM HEPES pH 6.6 plus 4 microliter reservoir solution, against a reservoir of 1 ml 34% PEG200, 600 mM CaCl2 and 10 mM HEPES pH 8.6.
Crystal Properties Matthews coefficient Solvent content 2.17 43.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.926 α = 90 b = 36.926 β = 90 c = 162.362 γ = 120
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 PILATUS3 6M 2018-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.8 31.41 92.2 0.081 0.099 0.056 0.995 3.5 3 3898
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 56.7 4.463 5.447 3.066 0.237 2.5
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 FOURIER SYNTHESIS THROUGHOUT 6QT1 1.8 31.4 3708 187 91.3 0.2352 0.2316 0.2287 0.3104 0.3091 RANDOM 55.095
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] 0.88 0.44 0.88 -2.86
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.71 r_angle_other_deg 1.661 r_chiral_restr 0.088 r_gen_planes_refined 0.021 r_bond_refined_d 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 325 Solvent Atoms 40 Heterogen Atoms 6
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction MOLREP phasing