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1A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING AND GROOVE-SPECIFIC BENDING OF DNA BY MAGNESIUM AND CALCIUM.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DNB BDJ019
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 275 initial concentration in droplet: 0.17 mM dna, 31.40 mM magnesium acetate
0.28 mM streptonigrin, 10-15% MPD, 30% final MPD concentration in reservoir.
Solutions were unbuffered, VAPOR DIFFUSION, SITTING DROP, temperature 275.0K
Crystal Properties Matthews coefficient Solvent content 2.06 36.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.243 α = 90 b = 25.352 β = 117.17 c = 34.19 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 100 AREA DETECTOR MARRESEARCH 1998-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C NSLS X8C
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 0.985 8 93.3 0.031 32.8 4.87 13087 13087 -1 5.82
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) 0.985 1.016 89.5 0.122 6.9 1253
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 BDJ019 0.985 8 13087 13087 654 93.3 0.1405 0.1405 0.1444 0.1509 0.1557 random
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 9 113 271.4
RMS Deviations Key Refinement Restraint Deviation s_angle_d 0.053 s_anti_bump_dis_restr 0.041 s_approx_iso_adps 0.039 s_similar_adp_cmpnt 0.023 s_bond_d 0.018 s_rigid_bond_adp_cmpnt 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 385 Solvent Atoms 51 Heterogen Atoms 48
Software Software Software Name Purpose X-PLOR model building SHELXL-97 refinement DENZO data reduction SCALEPACK data scaling X-PLOR phasing