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Crystal Structure of Z-DNA with 6-fold Twinning_Z4A
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 293 Percipient: 200 mM CaCl2, 50 mM Tris-HCl pH 7.0, 10% MPD
Reservior: 50% MPD
Crystal Properties Matthews coefficient Solvent content 1.65 25.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.43 α = 90 b = 44 β = 119.83 c = 35.43 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 2015-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.9756 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 31 99.1 0.075 13.8 3.7 22010
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 98.8 0.405 0.752 2.2 3.6
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 30.74 20986 1020 94.64 0.16888 0.16805 0.1705 0.18418 0.1967 RANDOM 24.546
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] -3.59 4.06 12.85 -9.27
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.741 r_sphericity_bonded 20.135 r_long_range_B_refined 5.046 r_scangle_other 4.861 r_long_range_B_other 4.729 r_scbond_other 3.924 r_scbond_it 3.923 r_rigid_bond_restr 3.688 r_angle_other_deg 1.761 r_angle_refined_deg 1.514
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.741 r_sphericity_bonded 20.135 r_long_range_B_refined 5.046 r_scangle_other 4.861 r_long_range_B_other 4.729 r_scbond_other 3.924 r_scbond_it 3.923 r_rigid_bond_restr 3.688 r_angle_other_deg 1.761 r_angle_refined_deg 1.514 r_chiral_restr 0.087 r_gen_planes_refined 0.017 r_gen_planes_other 0.011 r_bond_refined_d 0.01 r_bond_other_d 0.003 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 960 Solvent Atoms 162 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing