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Ultrahigh-resolution crystal structure of Z-DNA in complex with Zn2+ ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I0T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 292 A 1.5 MM DNA WATER SOLUTION MIXED 1:1 V/V WITH 10% MPD, 12 MM SPERMINE TETRA-HCL,12 MM NACL, 80 MM KCL AND EQUILIBRATED AGAINST 35% MPD, PH 6. VAPOR DIFFUSION, HANGING DROP METHOD, TEMPERATURE 292K. FOR ZN2+ SOAKING A CRYSTAL WAS PLACED IN 0.002 ML OF THE RESERVOIR SOLUTION MIXED WITH 0.002 ML OF 5 MM ZNCL2 FOR ONE WEEK.
Crystal Properties Matthews coefficient Solvent content 1.53 19.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 17.791 α = 90 b = 30.907 β = 90 c = 44.196 γ = 90
Symmetry Space Group P 21 21 21
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 MAR555 FLAT PANEL 2010-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 0.849 17.976 87.9 0.036 20.02 3.02 36512 -3 8.109
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) 1 0.85 0.9 63.8 0.222 3.11 1.77
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R 1I0T 0.85 17.976 36512 1004 87.9 0.092 0.092 0.113 0.1105 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 6 144.6 313.39
RMS Deviations Key Refinement Restraint Deviation s_anti_bump_dis_restr 0.123 s_approx_iso_adps 0.076 s_angle_d 0.059 s_similar_adp_cmpnt 0.033 s_bond_d 0.027 s_rigid_bond_adp_cmpnt 0.025 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 240 Solvent Atoms 75 Heterogen Atoms 17
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing SHELXL-97 refinement XDS data reduction XDS data scaling