5E3B
Structure of macrodomain protein from Streptomyces coelicolor
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | 0.1 M Tris-HCl, 0.29 M sodium chloride, 1.0 M sodium citrate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.58 | 52.25 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 103.819 | α = 90 |
b = 103.819 | β = 90 |
c = 33.254 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 | 2015-05-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ELETTRA BEAMLINE 5.2R | 0.976 | ELETTRA | 5.2R |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 46.43 | 97.9 | 0.12 | 0.043 | 0.997 | 11.5 | 8.6 | 24097 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.6 | 1.63 | 89.5 | 1.18 | 0.433 | 0.67 | 1.8 | 8.1 | 1057 |
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 | 2FG1 | 1.6 | 46.43 | 22860 | 1196 | 97.76 | 0.1861 | 0.1842 | 0.2233 | RANDOM | 19.9 |
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] | |
0.41 | 0.41 | -0.82 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 23.125 |
r_dihedral_angle_4_deg | 17.252 |
r_dihedral_angle_3_deg | 12.684 |
r_dihedral_angle_1_deg | 6.081 |
r_mcangle_it | 3.289 |
r_mcbond_it | 2.406 |
r_mcbond_other | 2.405 |
r_angle_refined_deg | 2.252 |
r_angle_other_deg | 1.175 |
r_chiral_restr | 0.142 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1128 |
Nucleic Acid Atoms | |
Solvent Atoms | 161 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |