5PQ5
PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 42)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 0.1M bis-tris pH 7.0 -- 30% PEG3350 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.16 | 43.14 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 55.164 | α = 90 |
b = 56.236 | β = 90 |
c = 101.66 | 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 | 100 | PIXEL | DECTRIS PILATUS 2M | 2014-08-28 | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.9200 | Diamond | I04-1 |
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 | 1.6 | 21.39 | 97.8 | 0.093 | 0.102 | 0.042 | 0.992 | 10.6 | 5.8 | 41451 |
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 | 1.6 | 1.69 | 95.2 | 0.707 | 0.789 | 0.341 | 0.704 | 5 | 5785 |
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 | FOURIER SYNTHESIS | THROUGHOUT | 5AMF | 1.6 | 21.39 | 39362 | 2043 | 97.38 | 0.1874 | 0.1856 | 0.2226 | RANDOM | 20.293 |
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] | |
1.63 | -0.75 | -0.89 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.775 |
r_dihedral_angle_4_deg | 14.216 |
r_dihedral_angle_3_deg | 13.278 |
r_dihedral_angle_1_deg | 4.778 |
r_mcangle_it | 2.739 |
r_mcbond_it | 2.026 |
r_mcbond_other | 2.006 |
r_angle_refined_deg | 1.936 |
r_angle_other_deg | 1.107 |
r_chiral_restr | 0.126 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1953 |
Nucleic Acid Atoms | |
Solvent Atoms | 259 |
Heterogen Atoms | 21 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
REFMAC | phasing |