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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: 0.24 MM DNA, 8.57 MM MAGNESIUM ACETATE, 0.11 MM STREPTONIGRIN, 10-15% MPD, 45% FINAL MPD CONCENTRATION IN RESERVOIR. SOLUTIONS WERE UNBUFFERED, VAPOR DIFFUSION, SITTING DROP, temperature 275.0K
Crystal Properties Matthews coefficient Solvent content 2.08 37.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.001 α = 90 b = 25.369 β = 112.98 c = 33.633 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 IMAGE PLATE 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 95 0.047 21.6 5.75 13464 13464 -1 5.3
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) 0.985 1.016 90.7 0.123 7.4
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 13464 13464 631 95 0.1409 0.1409 0.1477 0.1592 0.1654 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 14 114 272.84
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.072 s_angle_d 0.049 s_similar_adp_cmpnt 0.026 s_anti_bump_dis_restr 0.019 s_bond_d 0.018 s_rigid_bond_adp_cmpnt 0.006 s_similar_dist s_from_restr_planes s_zero_chiral_vol s_non_zero_chiral_vol
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 364 Solvent Atoms 61 Heterogen Atoms 32
Software Software Software Name Purpose X-PLOR model building SHELXL-97 refinement DENZO data reduction SCALEPACK data scaling X-PLOR phasing