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Racemic crystal structure of a calcium-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, 2 M calcium chloride, 1 mM spermine, 40% v/v MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.07 40.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 23.263 α = 103.32 b = 33.604 β = 101.02 c = 36.82 γ = 109.78
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 2M-F 2014-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
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 1.28 34.25 95.23 0.0372 9.69 1.9 25176 23975 2 2 47.43
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 1.28 1.32 91.68 0.2656 2.39 1.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3R86 1.28 34.25 22744 1230 95.23 0.21889 0.21655 0.25957 0.272 RANDOM 14.318
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] 0.61 -0.61 0.54 -0.47 -0.33 0.28
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 25.398 r_sphericity_bonded 12.844 r_rigid_bond_restr 7.152 r_angle_refined_deg 1.854 r_chiral_restr 0.11 r_gen_planes_refined 0.031 r_bond_refined_d 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 404 Solvent Atoms 167 Heterogen Atoms 9
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement XDS data reduction d*TREK data scaling