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Racemic crystal structure of a magnesium-bound B-DNA duplex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R86 PDB ENTRY 3R86
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1 mM DNA, 50 mM sodium cacodylate, 200 mM magnesium chloride, 2.5 mM spermine, 30% v/v MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.79 31.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.61 α = 70.76 b = 32.951 β = 80.77 c = 46.25 γ = 73.77
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 PILATUS 6M 2014-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9998 SOLEIL PROXIMA 1
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 1.29 43.54 91.4 0.023 14.11 1.9 42395 38749 2 2 47.68
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.29 1.37 86.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 3R86 1.29 43.54 40186 37851 1979 94.19 0.2709 0.2689 0.2699 0.3113 0.3133 RANDOM 18.519
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] 0.25 0.2 -0.03 -0.54 0.16 0.48
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 14.304 r_sphericity_bonded 10.356 r_rigid_bond_restr 9.989 r_angle_refined_deg 2.298 r_chiral_restr 0.121 r_gen_planes_refined 0.028 r_bond_refined_d 0.013 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 14.304 r_sphericity_bonded 10.356 r_rigid_bond_restr 9.989 r_angle_refined_deg 2.298 r_chiral_restr 0.121 r_gen_planes_refined 0.028 r_bond_refined_d 0.013 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 808 Solvent Atoms 134 Heterogen Atoms 9
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement XDS data reduction d*TREK data scaling