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Structure of B-DNA d(CGTTAATTAACG)2 in the presence of Manganese
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 463D PDB entry 463d
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 289 25 mM Sodium Cacodylate, 10 mM Manganese, 25 mM spermine, 25 % MPD,0,1 mM DNA, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.48 50.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.795 α = 90 b = 43.795 β = 90 c = 98.345 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 2007-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 0.97827 ESRF BM16
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 2.41 37.93 99.6 0.051 4.6 6489 6461 -3
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) 2.59 2.7 99.3 0.795 4.2
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 463d 2.6 37.93 6489 6146 316 99.57 0.23679 0.23465 0.2491 0.28471 0.303 RANDOM 56.315
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] 4.34 2.17 4.34 -6.5
RMS Deviations Key Refinement Restraint Deviation r_scbond_it 11.637 r_scangle_it 11.061 r_angle_other_deg 1.511 r_angle_refined_deg 1.398 r_chiral_restr 0.055 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_dihedral_angle_1_deg
RMS Deviations Key Refinement Restraint Deviation r_scbond_it 11.637 r_scangle_it 11.061 r_angle_other_deg 1.511 r_angle_refined_deg 1.398 r_chiral_restr 0.055 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1362 Solvent Atoms 34 Heterogen Atoms 7
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling