Z-DNA joint X-ray/Neutron
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) |
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Type | Source | Accession Code | Details |
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experimental model | PDB | 3QBA | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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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 |
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Matthews coefficient | Solvent content |
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1.7 | 27.69 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 17.96 | α = 90 |
b = 31.15 | β = 90 |
c = 44.03 | γ = 90 |
Symmetry |
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Space Group | P 21 21 21 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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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 |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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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 |
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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 |
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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 |
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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) |
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1 | 1.5 | 1.55 | | | | | | 0.482 | | | 3.85 | |
2 | 1 | 1.08 | | | | | | 0.985 | | | 7.8 | |
Refinement
Statistics |
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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 | R-Free | R-Free Selection Details | Mean Isotropic B |
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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 | 0.185 | | 25.37 |
Temperature Factor Modeling |
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
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RMS Deviations |
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Key | Refinement Restraint Deviation |
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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 |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | |
Nucleic Acid Atoms | 240 |
Solvent Atoms | 77 |
Heterogen Atoms | |
Software
Software |
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Software Name | Purpose |
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PHENIX | refinement |
SAINT | data reduction |
Aimless | data scaling |
PHENIX | phasing |