5NO6
TEAD4-HOXB13 complex bound to DNA
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5EEA | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.24 | 298 | PEG (4000), Ammonium sulphate, PME(550, MOPs |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.13 | 60.72 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 82.659 | α = 90 |
| b = 56.674 | β = 93.81 |
| c = 144.993 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 1 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 | ADSC QUANTUM 315r | 2016-04-21 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.97242 | ESRF | ID23-1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.88 | 46.71 | 95.1 | 0.039 | 0.049 | 0.029 | 1 | 12 | 2.4 | 14626 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 2.88 | 3.06 | 94.8 | 1.845 | 2.288 | 1.331 | 0.257 | 2.4 | |||||||||||
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 | 5EEA | 2.88 | 45 | 13860 | 765 | 95.04 | 0.24371 | 0.23955 | 0.31677 | RANDOM | 125.688 | ||||||
| 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] | |
| 2.99 | 3.45 | 1.42 | -4.82 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.051 |
| r_dihedral_angle_1_deg | 29.575 |
| r_dihedral_angle_3_deg | 22.732 |
| r_long_range_B_refined | 16.968 |
| r_long_range_B_other | 16.968 |
| r_dihedral_angle_4_deg | 14.822 |
| r_mcangle_it | 14.274 |
| r_mcangle_other | 14.268 |
| r_scangle_other | 11.776 |
| r_mcbond_it | 8.836 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2230 |
| Nucleic Acid Atoms | 1476 |
| Solvent Atoms | 16 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| Aimless | data scaling |
| PHASER | phasing |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
