☰ Navigation Tabs
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 2.65 53.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.989 α = 90 b = 25.989 β = 90 c = 121.531 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 0.979200 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 2.1 22.51 97.8 0.138 16.3 10.6 3035
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 2.1 2.17 97.4 0.244 3 3
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 2.1 40.51 2716 301 95.81 0.27493 0.27086 0.276 0.31152 0.3189 RANDOM 53.965
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] 0.04 0.02 0.04 -0.14
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 5.663 r_long_range_B_refined 5.662 r_scangle_other 4.456 r_angle_other_deg 3.352 r_scbond_it 2.651 r_scbond_other 2.647 r_angle_refined_deg 1.406 r_chiral_restr 0.177 r_gen_planes_refined 0.009 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 5.663 r_long_range_B_refined 5.662 r_scangle_other 4.456 r_angle_other_deg 3.352 r_scbond_it 2.651 r_scbond_other 2.647 r_angle_refined_deg 1.406 r_chiral_restr 0.177 r_gen_planes_refined 0.009 r_bond_refined_d 0.006 r_bond_other_d 0.002 r_gen_planes_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 293 Solvent Atoms 13 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data scaling Aimless data scaling PHENIX refinement