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Z-DNA joint X-ray/Neutron
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QBA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2.5 M (ND4)2SO4, 10 mM magnesium acetate, 50 mM perdeuterated 2-(N-morpholino)ethanesulfonic acid (MES)
Crystal Properties Matthews coefficient Solvent content 1.7 27.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 17.96 α = 90 b = 31.15 β = 90 c = 44.03 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 neutron 100 AREA DETECTOR ORNL ANGER CAMERA 2018-10-24 L LAUE 2 1 x-ray 100 PIXEL Bruker PHOTON II 2019-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SPALLATION SOURCE ORNL Spallation Neutron Source BEAMLINE MANDI 2.0-6.0 ORNL Spallation Neutron Source MANDI 2 LIQUID ANODE Excillum MetalJet D2+ 70 kV 1.3418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 1.5 14.67 84.2 0.918 13.8 5.89 3587 5.53 2 1 18 95.9 0.999 12.8 10.5 18334 3.04
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.55 0.482 3.85 2 1 1.08 0.985 7.8
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 1.5 14.67 3585 84.02 0.277 0.303 X-RAY DIFFRACTION MOLECULAR REPLACEMENT 1 18 18307 2507 95.9 0.1593 0.1563 0.1573 0.185 0.1856 25.37
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 28.5895 f_dihedral_angle_d 28.5895 f_angle_d 1.4385 f_angle_d 1.4385 f_chiral_restr 0.0768 f_chiral_restr 0.0768 f_plane_restr 0.0118 f_plane_restr 0.0118 f_bond_d 0.0116 f_bond_d 0.0116
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 240 Solvent Atoms 77 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement SAINT data reduction Aimless data scaling PHENIX phasing