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Crystal Structure Analysis of the B-DNA GAATTCG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other ideal B-DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 MPD, Nickel Chloride, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.47 64.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.867 α = 90 b = 70.867 β = 90 c = 70.867 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 CCD MARRESEARCH 2002-09-10 2 1 x-ray CCD MARRESEARCH 2002-09-10 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 1.00000 ESRF BM14 2 SYNCHROTRON ESRF BEAMLINE BM14 1.48475, 1.48563, 1.31155 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 2.81 22.4 97.4 0.095 1491
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT ideal B-DNA 2.81 22.4 1388 69 95.73 0.281 0.281 0.281 0.26428 0.2031 RANDOM 36.94
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 r_scangle_it 4.73 r_angle_refined_deg 3.124 r_scbond_it 2.89 r_mcbond_it 0.568 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.202 r_chiral_restr 0.1 r_symmetry_hbond_refined 0.078 r_bond_refined_d 0.019
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.73 r_angle_refined_deg 3.124 r_scbond_it 2.89 r_mcbond_it 0.568 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.202 r_chiral_restr 0.1 r_symmetry_hbond_refined 0.078 r_bond_refined_d 0.019 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 284 Solvent Atoms 20 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SHELXD phasing SHELXE model building