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Photo-crosslinkable oligonucleotodes which have a trioxsalen conjugated to C2' position of guanosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QJS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 297 MOPS pH7, Spermine, Sodium Chloride, MPD
Crystal Properties Matthews coefficient Solvent content 3.74 67.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.385 α = 90 b = 49.385 β = 90 c = 66.946 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 173 PIXEL DECTRIS EIGER X 16M 2023-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 3.11 39.74 99 0.059000000000000004 0.061 0.9990000000000001 38.79 22.7 1679
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.11 3.21 0.081 0.084 0.9990000000000001
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 3.11 39.74 1.36 1649 162 97.11 0.2976 0.2943 0.2943 0.3254 0.3252
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 34.858 f_angle_d 2.246 f_chiral_restr 0.21 f_plane_restr 0.053 f_bond_d 0.017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 368 Solvent Atoms Heterogen Atoms 82
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling XDS data reduction PHASER phasing