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Crosslinking of DNA duplexes: X-ray crystal structure of an unsubstituted bisacridine with the oligonucleotide d(CGTACG)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C9Z NDB ENTRY DD0018
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 The crystals grow in ten days from sitting drops containing 2mM DNA, 12mM spermine, 80mM strontium chloride, 20mM magnesium chloride, 10%MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 38.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.75 α = 90 b = 25.75 β = 90 c = 78.994 γ = 120
Symmetry Space Group P 65 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 1.0 EMBL/DESY, HAMBURG X12
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 22.3 99.3 0.038 49.4 20.1 1472 2 2 57.431
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 2 100 0.312 9 15.3 204
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 (All) 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 NDB ENTRY DD0018 2.2 8 890 45 99.36 0.358 0.27223 0.27002 0.2629 0.30508 0.3339 RANDOM 37.613
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] 2.09 1.05 2.09 -3.14
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.224 r_scbond_it 3.483 r_angle_refined_deg 3.391 r_nbtor_refined 0.371 r_symmetry_vdw_refined 0.322 r_nbd_refined 0.274 r_symmetry_hbond_refined 0.216 r_chiral_restr 0.165 r_bond_refined_d 0.022 r_gen_planes_refined 0.017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 120 Solvent Atoms 1 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction MOLREP phasing