3MLO
DNA binding domain of Early B-cell Factor 1 (Ebf1) bound to DNA (Crystal form I)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5.7 | 293 | 6% PEG4000, 200mM KCl, 100mM MES, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.35 | 63.32 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 70.75 | α = 90 |
| b = 70.75 | β = 90 |
| c = 601.56 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 65 2 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | CCD | MARMOSAIC 225 mm CCD | 2009-08-03 | M | SINGLE WAVELENGTH | |||||||
| 2 | 1 | x-ray | CCD | MARMOSAIC 225 mm CCD | 2009-08-03 | M | MAD | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SLS BEAMLINE X06DA | 1.0000 | SLS | X06DA |
| 2 | SYNCHROTRON | SLS BEAMLINE X06DA | 1.2551, 1.2556, 1.2425 | SLS | X06DA |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 3 | 30 | 98.9 | 0.182 | 11.8 | 13.1 | 19386 | 19172 | 2 | 41.7 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1,2 | 3 | 3.1 | 89.9 | 0.591 | 2.6 | 9.9 | 1744 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | MAD | THROUGHOUT | 3.01 | 29.71 | 19172 | 18211 | 959 | 100 | 0.22387 | 0.221 | 0.27778 | RANDOM | 60.109 | ||||||
| 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] | |
| 1.35 | 0.68 | 1.35 | -2.03 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.319 |
| r_dihedral_angle_4_deg | 19.337 |
| r_dihedral_angle_3_deg | 19.009 |
| r_dihedral_angle_1_deg | 6.526 |
| r_scangle_it | 1.633 |
| r_angle_refined_deg | 1.341 |
| r_scbond_it | 0.979 |
| r_mcangle_it | 0.711 |
| r_mcbond_it | 0.368 |
| r_chiral_restr | 0.077 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3411 |
| Nucleic Acid Atoms | 896 |
| Solvent Atoms | 33 |
| Heterogen Atoms | 2 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SHARP | phasing |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
