8A5S
Crystal structure of light-activated DNA-binding protein EL222 from Erythrobacter litoralis crystallized in dark, measured illuminated.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 291.15 | 21% (w/v) PEG 8000, 0.22 M MgCl2, 0.11 M MES pH 6.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.96 | 37.33 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43.426 | α = 90 |
b = 51.852 | β = 90 |
c = 80.381 | γ = 90 |
Symmetry | |
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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 | Bruker PHOTON II | HELIOS optics for MetalJet | 2020-06-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | LIQUID ANODE | Excillum MetalJet D2 70 kV | 1.3418 |
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 | 1.85 | 43.57 | 99.7 | 0.116 | 0.129 | 0.055 | 0.996 | 10.9 | 5.2 | 16065 | 9.6 |
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 | 1.85 | 1.89 | 99.9 | 0.772 | 0.881 | 0.418 | 0.636 | 1.9 | 4.2 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3P7N | 1.85 | 40.223 | 16016 | 815 | 99.565 | 0.161 | 0.1613 | 0.1606 | 0.2154 | Random selection | 17.705 |
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] | |
0.482 | -0.476 | -0.006 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.37 |
r_dihedral_angle_other_3_deg | 23.857 |
r_dihedral_angle_4_deg | 18.015 |
r_dihedral_angle_3_deg | 14.785 |
r_lrange_it | 5.808 |
r_dihedral_angle_1_deg | 5.774 |
r_lrange_other | 5.567 |
r_scangle_it | 3.489 |
r_scangle_other | 3.487 |
r_mcangle_it | 2.481 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1602 |
Nucleic Acid Atoms | |
Solvent Atoms | 223 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PROTEUM PLUS | data collection |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |
Coot | model building |