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X-ray crystal structure of a continuously hydrogen bonded 14mer DNA lattice.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BXW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 296.15 120mM Magnesium Formate
50mM Lithium Chloride
10% MPD
Crystal Properties Matthews coefficient Solvent content 2.64 53.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.958 α = 90 b = 25.958 β = 90 c = 121.533 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77.15 PIXEL PSI PILATUS 6M 2014-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97920 APS 24-ID-C
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 2.4 22.48 99.1 0.093 8.9 3.8 2131
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 2.4 2.53 98.7 0.208 2.6 3.5
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 5BXW 2.4 40.51 1898 194 97.67 0.25046 0.24536 0.2447 0.31275 0.3172 RANDOM 49.278
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 34.367 r_angle_other_deg 2.817 r_long_range_B_other 1.923 r_long_range_B_refined 1.922 r_scangle_other 1.263 r_angle_refined_deg 1.22 r_rigid_bond_restr 1.134 r_scbond_it 0.74 r_scbond_other 0.739 r_chiral_restr 0.135
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 34.367 r_angle_other_deg 2.817 r_long_range_B_other 1.923 r_long_range_B_refined 1.922 r_scangle_other 1.263 r_angle_refined_deg 1.22 r_rigid_bond_restr 1.134 r_scbond_it 0.74 r_scbond_other 0.739 r_chiral_restr 0.135 r_gen_planes_refined 0.008 r_gen_planes_other 0.007 r_bond_refined_d 0.005 r_bond_other_d 0.001 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 r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 293 Solvent Atoms 6 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement PHENIX refinement Aimless data scaling XDS data scaling PHASER phasing