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Crystal structure of Z-DNA in complex with putrescinium and potassium cations at ultrahigh-resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HIG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 292 10%(v/v) (+/-)-2-methyl-2,4-pentanediol (MPD), 40 mM sodium cacodylate pH 6.0, 80 mM KCl, 12 mM NaCl, 14 mM putrescinium dichloride
Crystal Properties Matthews coefficient Solvent content 1.8 31.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 17.97 α = 90 b = 31.02 β = 90 c = 43.86 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 PIXEL DECTRIS PILATUS3 S 6M 2015-06-22 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2015-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.72930 PETRA III, EMBL c/o DESY P13 (MX1) 2 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.7293 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 0.6 25.33 90.5 0.024 0.027 0.999 29.84 3.7 107989 5.17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.6 0.61 22.6 0.264 0.368 0.999 2.88 1.2
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 FREE R-VALUE 4hig 0.6 25.33 106103 1876 90.5 0.0888 0.0877 0.0976 0.095 RANDOM 6.26
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 3 141.29 333.73
RMS Deviations Key Refinement Restraint Deviation s_angle_d 1.56 s_anti_bump_dis_restr 0.089 s_approx_iso_adps 0.07 s_similar_adp_cmpnt 0.061 s_bond_d 0.01 s_from_restr_planes 0.005 s_similar_dist s_zero_chiral_vol s_non_zero_chiral_vol s_rigid_bond_adp_cmpnt
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 240 Solvent Atoms 159 Heterogen Atoms 7
Software Software Software Name Purpose SHELXL refinement XDS data reduction XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction