Crystal structure of RNA:DNA dodecamer corresponding to HIV-1 polypurine tract, at 1.6 A resolution.
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1PJO | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 5.5 | 292 | 40% MPD, 0.04M hexamminecobalt(III) chloride, 0.02M magnesium chloride, 0.04M lithium chloride, 0.04M sodium cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.94 | 36.7 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 41.904 | α = 90 |
| b = 41.904 | β = 90 |
| c = 57.24 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 32 2 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | CCD | MAR CCD 165 mm | 2009-12-04 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X13 | EMBL/DESY, HAMBURG | X13 | |
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 | 1.6 | 50 | 99.5 | 0.04 | 41.7 | 6.7 | 8012 | -3 | |||||||||||
| 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 | 1.6 | 1.66 | 99.6 | 0.55 | 2.851 | 5.5 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | 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 | THROUGHOUT | 1PJO | 1.6 | 15.32 | 7994 | 7204 | 790 | 99.5 | 0.186 | 0.181 | 0.19 | 0.229 | 0.24 | RANDOM | 23.02 | |||
| 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] | |
| 0.25 | 0.13 | 0.25 | -0.38 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_angle_refined_deg | 2.258 |
| r_angle_other_deg | 1.758 |
| r_gen_planes_refined | 0.033 |
| r_bond_refined_d | 0.02 |
| r_bond_other_d | 0.011 |
| r_gen_planes_other | 0.009 |
| r_dihedral_angle_1_deg | |
| r_dihedral_angle_2_deg | |
| r_dihedral_angle_3_deg | |
| r_dihedral_angle_4_deg | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | |
| Nucleic Acid Atoms | 497 |
| Solvent Atoms | 76 |
| Heterogen Atoms | 3 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MAR345dtb | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
