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 | 0.16 | 0.185 | 0.19 | | 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 |
