Low Temperature joint X-ray/neutron structure of DNA oligonucleotide d(GTGGCCAC)2 with 2'-SeCH3 modification on Cyt5
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 4FP6 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 303 | 0.1 M magnesium acetate, 30% MPD, 0.1 M MES |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.06 | 40.38 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 41.884 | α = 90 |
| b = 41.884 | β = 90 |
| c = 24.307 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 43 21 2 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS IV++ | osmic varimax | 2017-12-12 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 100 | IMAGE PLATE | LADI III | collimators | 2017-11-20 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54 | | |
| 2 | NUCLEAR REACTOR | ILL BEAMLINE LADI III | 2.8-4.0 | ILL | LADI III |
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 | 1.65 | 40 | 100 | 0.056 | | | | | | 16.6 | 10.4 | | 2866 | | | |
| 2 | 1.9 | 21.3 | 84.6 | 0.179 | | | | | | 9.1 | 7 | | 1629 | | | |
| 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 | 1.65 | 1.71 | | 0.149 | | | | | | | 10.2 | |
| 2 | 1.9 | 2 | | 0.226 | | | | | | | 3.4 | |
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 |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.65 | 40 | | 2.5 | 2843 | 2800 | 136 | 98.2 | | | 0.23 | 0.26 | 0.246 | 0.26 | random | 24.54 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.9 | 21.3 | | 2.5 | 1909 | 1572 | 65 | 82.3 | | | 0.234 | | 0.26 | | random | 24.54 |
| 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 |
|---|
| x_torsion_impr_deg | 0.95 |
| x_torsion_impr_deg | 0.95 |
| x_angle_deg | 0.9 |
| x_angle_deg | 0.9 |
| x_torsion_deg | 0.7 |
| x_torsion_deg | 0.7 |
| x_bond_d | 0.006 |
| x_bond_d | 0.006 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 163 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 39 |
| Heterogen Atoms | 2 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| nCNS | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| PHASER | phasing |
| LAUEGEN | data reduction |
| LSCALE | data scaling |
| CNS | phasing |
