5PSO
PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 132)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 0.1M bis-tris pH 7.0 -- 30% PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 43.64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.356 | α = 90 |
b = 56.435 | β = 90 |
c = 101.844 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | |||||||||||||||||||
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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 | 1.55 | 29.09 | 98.2 | 0.074 | 0.08 | 0.031 | 0.999 | 14.9 | 6.7 | 46317 |
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 | 1.55 | 1.59 | 97.4 | 0.817 | 0.887 | 0.339 | 0.775 | 6.6 | 3353 |
Refinement
Statistics | |||||||||||||||||||
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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 | 1.55 | 29.09 | 43991 | 2272 | 97.83 | 0.1832 | 0.1817 | 0.2123 | RANDOM | 21.777 |
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] | |
1.17 | -0.34 | -0.83 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.289 |
r_dihedral_angle_3_deg | 13.723 |
r_dihedral_angle_4_deg | 13.417 |
r_dihedral_angle_1_deg | 4.576 |
r_mcangle_it | 2.784 |
r_mcbond_it | 1.988 |
r_angle_refined_deg | 1.983 |
r_mcbond_other | 1.973 |
r_angle_other_deg | 1.095 |
r_chiral_restr | 0.125 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1953 |
Nucleic Acid Atoms | |
Solvent Atoms | 259 |
Heterogen Atoms | 21 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
REFMAC | phasing |