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Crystal Structure of Z-DNA with 6-fold Twinning_Z3B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P4J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 100 mM KCl, 10 mM MgCl2, Tris-HCl pH 8.5, 30% PEG 400
Crystal Properties Matthews coefficient Solvent content 1.61 23.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.84 α = 90 b = 42.57 β = 120.05 c = 30.84 γ = 90
Symmetry Space Group P 1 21 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 CCD RAYONIX MX300-HS 2017-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
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 1.3 27 99.2 0.063 23.5 7 17047
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.35 97.9 0.646 0.82 2.5 6.4
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3P4J 1.3 26.71 16198 834 98.97 0.13183 0.1309 0.13 0.14742 0.1409 RANDOM 26.875
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] -12.14 4.67 11.15 0.99
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 28.835 r_sphericity_bonded 24.265 r_long_range_B_refined 6.904 r_long_range_B_other 6.833 r_scangle_other 6.41 r_rigid_bond_restr 5.707 r_scbond_other 4.937 r_scbond_it 4.935 r_angle_other_deg 1.96 r_angle_refined_deg 1.587
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 28.835 r_sphericity_bonded 24.265 r_long_range_B_refined 6.904 r_long_range_B_other 6.833 r_scangle_other 6.41 r_rigid_bond_restr 5.707 r_scbond_other 4.937 r_scbond_it 4.935 r_angle_other_deg 1.96 r_angle_refined_deg 1.587 r_chiral_restr 0.096 r_gen_planes_other 0.019 r_gen_planes_refined 0.018 r_bond_refined_d 0.01 r_bond_other_d 0.002 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 720 Solvent Atoms 77 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing