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Crystal Structure Analysis of the B-DNA Decamer CGCAATTGCG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 237D NDB ENTRY UDJ031
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 MPD, acridine(RGR), cacodylate, calcium chloride, cobalt chloride, spermine , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.56 51.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.22 α = 90 b = 44.359 β = 90 c = 52.336 γ = 90
Symmetry Space Group I 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.917 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.6 25 98.4 0.061 0.077 17.7 4174
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.66 89.1 0.23 0.6 2.93 376
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 UDJ031 1.6 22.59 3746 414 97.86 0.214 0.21601 0.20969 0.2206 0.28152 0.2814 RANDOM 24.833
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] -0.02 2.26 -2.24
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.387 r_angle_refined_deg 2.595 r_scbond_it 2.305 r_angle_other_deg 1.431 r_symmetry_vdw_other 0.354 r_symmetry_vdw_refined 0.279 r_nbd_other 0.19 r_xyhbond_nbd_refined 0.182 r_symmetry_hbond_refined 0.158 r_nbd_refined 0.13
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.387 r_angle_refined_deg 2.595 r_scbond_it 2.305 r_angle_other_deg 1.431 r_symmetry_vdw_other 0.354 r_symmetry_vdw_refined 0.279 r_nbd_other 0.19 r_xyhbond_nbd_refined 0.182 r_symmetry_hbond_refined 0.158 r_nbd_refined 0.13 r_nbtor_other 0.098 r_chiral_restr 0.082 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 211 Solvent Atoms 47 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing