4RP0
Sequence and structure of a self-assembled 3-D DNA crystal: D(GGATAATTAGGAG)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | EVAPORATION | 298 | Self-assembling 3D DNA crystal 120mM Magnesium Formate, 50mM Lithium Chloride, 10% MPD, pH none, EVAPORATION, temperature 298K | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.03 | 59.37 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 40.177 | α = 90 |
| b = 40.177 | β = 90 |
| c = 53.015 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 64 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M-F | 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 | 2.19 | 34.79 | 0.024 | 31.2 | 5.5 | 2540 | |||||||||||||
| 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 | 2.19 | 2.31 | 1.369 | 1.1 | 5.3 | 375 | |||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1p1y | 2.19 | 34.79 | 2285 | 217 | 98.19 | 0.22308 | 0.2223 | 0.23105 | RANDOM | 97.421 | ||||||
| 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] | |
| 0.48 | 0.24 | 0.48 | -1.55 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_long_range_B_refined | 10.755 |
| r_long_range_B_other | 10.743 |
| r_scangle_other | 8.173 |
| r_scbond_other | 4.699 |
| r_scbond_it | 4.685 |
| r_angle_other_deg | 1.705 |
| r_angle_refined_deg | 1.081 |
| r_chiral_restr | 0.077 |
| r_gen_planes_refined | 0.009 |
| r_bond_refined_d | 0.007 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | |
| Nucleic Acid Atoms | 254 |
| Solvent Atoms | 2 |
| Heterogen Atoms | 1 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
