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Locating monovalent cations in one turn of G/C rich B-DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BD1 DNA coordinates from PDB Entry 1bd1 (Heinemann and Alings)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 MPD, Magnesium acetate, Rubidium acetate, Rubidium hydroxide, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.03 39.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.135 α = 90 b = 25.156 β = 116.24 c = 34.113 γ = 90
Symmetry Space Group C 1 2 1
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 MARMOSAIC 300 mm CCD 2004-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.81528 APS 22-ID
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 0.784 30.6 63.9 0.074 23 6.2 19281
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT DNA coordinates from PDB Entry 1bd1 (Heinemann and Alings) 0.87 30.6 17543 17543 1047 90.55 0.11971 0.1188 0.1343 RANDOM 7.764
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] 0.2 -0.14 -0.14 -0.18
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 3.647 r_sphericity_free 3.401 r_angle_refined_deg 1.833 r_scangle_it 1.633 r_scbond_it 1.339 r_rigid_bond_restr 0.839 r_nbtor_refined 0.302 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.16 r_symmetry_hbond_refined 0.114
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 3.647 r_sphericity_free 3.401 r_angle_refined_deg 1.833 r_scangle_it 1.633 r_scbond_it 1.339 r_rigid_bond_restr 0.839 r_nbtor_refined 0.302 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.16 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.104 r_xyhbond_nbd_refined 0.099 r_gen_planes_refined 0.025 r_bond_refined_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 287 Solvent Atoms 156 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement CNS refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing