Joint nentron and X-ray structure of BRD4 in complex with colchicin
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | | 293 | 2.9M sodium formate, 17mM Tris, 83mM Tris-HCl in D2O |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.12 | 41.91 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 36.763 | α = 90 |
| b = 47.101 | β = 90 |
| c = 79.052 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 21 21 21 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 298 | CCD | ADSC QUANTUM 210r | | 2017-05-14 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 293 | IMAGE PLATE | BIODIFF | | 2018-02-12 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NW12A | 1 | Photon Factory | AR-NW12A |
| 2 | NUCLEAR REACTOR | FRM II BEAMLINE BIODIFF | 3.99 | FRM II | BIODIFF |
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 | 1.3 | 40.5 | 96.5 | | | | 0.022 | | | 18.9 | 6.1 | | 33279 | | | |
| 2 | 1.85 | 30.3 | 89.3 | | | | 0.071 | | | 7.8 | 2.5 | | 11030 | | | |
| 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 | 1.3 | 1.35 | | | | | 0.171 | | | | | |
| 2 | 1.85 | 1.9 | | | | | 0.294 | | | | | |
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 | | 1.301 | 30.278 | | 1.38 | | 33255 | 1663 | 96.55 | | 0.1638 | 0.163 | 0.16 | 0.1787 | 0.17 | | |
| NEUTRON DIFFRACTION | | 1.847 | 30.278 | | | | 11011 | 555 | 89.34 | | 0.2054 | 0.2039 | | 0.2346 | | | |
| 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 |
|---|
| f_dihedral_angle_d | 17.552 |
| f_dihedral_angle_d | 17.552 |
| f_angle_d | 1.412 |
| f_angle_d | 1.412 |
| f_chiral_restr | 0.32 |
| f_chiral_restr | 0.32 |
| f_bond_d | 0.01 |
| f_bond_d | 0.01 |
| f_plane_restr | 0.007 |
| f_plane_restr | 0.007 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1115 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 110 |
| Heterogen Atoms | 30 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| XDS | data reduction |
| HKL-2000 | data reduction |
| XSCALE | data scaling |
| SCALEPACK | data scaling |
| MOLREP | phasing |
