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Radiation damage study on a 16mer DNA segment, structure at 0.48 MGy dose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SGS
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 2.16 42.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.823 α = 90 b = 36.823 β = 90 c = 161.926 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 31.29 92.1 0.044 0.053 0.03 0.998 9.4 2.9 3861
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 59 0.779 0.959 0.549 0.608 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 MOLECULAR REPLACEMENT THROUGHOUT 1SGS 1.8 31.29 3671 180 91.21 0.2212 0.2196 0.2247 0.2555 0.2006 RANDOM 49.345
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] 0.87 0.44 0.87 -2.83
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.914 r_angle_other_deg 1.736 r_chiral_restr 0.094 r_gen_planes_refined 0.025 r_bond_refined_d 0.011 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 MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction