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Ultrahigh-resolution crystal structure of Z-DNA in complex with Mn2+ ion.
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 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 MN2+ SOAKING, A CRYSTAL WAS PLACED IN 0.002 ML OF THE RESERVOIR SOLUTION MIXED WITH 0.002 ML OF 5 MM MNCL2 FOR ONE WEEK.
Crystal Properties Matthews coefficient Solvent content 1.59 22.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 17.732 α = 90 b = 31.436 β = 90 c = 43.935 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 CCD MAR CCD 165 mm 2009-12-04 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD RAYONIX MX-225 2012-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 EMBL/DESY, HAMBURG X12 2 SYNCHROTRON BESSY BEAMLINE 14.2 BESSY 14.2
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 0.75 25.57 79.9 0.053 19.28 3.28 47730 -3 4.756
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 0.75 0.77 10.6 0.038 11.39 1.15
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R 1I0T 0.75 25.57 47730 1009 79.9 0.071 0.071 0.0792 0.081 0.0809 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 1 164 332.97
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.069 s_similar_adp_cmpnt 0.037 s_angle_d 0.029 s_anti_bump_dis_restr 0.028 s_bond_d 0.012 s_rigid_bond_adp_cmpnt 0.004 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 92 Heterogen Atoms 15
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing SHELXL-97 refinement XDS data reduction XSCALE data scaling