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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, Thallium acetate, Cacodylic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.04 39.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.277 α = 90 b = 25.204 β = 116.1 c = 34.095 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 IMAGE PLATE MAR scanner 300 mm plate 2004-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97582 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 0.92 30.6 76 0.143 61 7 13522
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-Work (DCC) 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) 0.98 15.31 11908 992 90.05 0.12019 0.1183 0.1167 0.14397 RANDOM 7.856
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] 0.1 -0.19 -0.1 -0.17
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 4.23 r_sphericity_bonded 3.329 r_angle_refined_deg 1.892 r_scangle_it 1.809 r_scbond_it 1.467 r_rigid_bond_restr 0.914 r_nbtor_refined 0.298 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.112
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 4.23 r_sphericity_bonded 3.329 r_angle_refined_deg 1.892 r_scangle_it 1.809 r_scbond_it 1.467 r_rigid_bond_restr 0.914 r_nbtor_refined 0.298 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.112 r_symmetry_hbond_refined 0.11 r_chiral_restr 0.106 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 140 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement CNS refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing