6GZ0
Crystal Structure of the LeuO Effector Binding Domain
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3OXN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 298 | 0.2 M Lithium sulfate, 0.1 M Bis-Tris pH 5.5, 25% polyethylene glycol 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.12 | 41.91 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.62 | α = 90 |
b = 61.22 | β = 106.24 |
c = 56.54 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | 2015-07-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 0.97942 | SLS | X06DA |
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 | 1.52 | 54.284 | 96.96 | 0.051 | 0.0059 | 0.029 | 0.998 | 10.3 | 4.1 | 31127 | 19.9 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.52 | 1.55 | 93.98 | 0.507 | 0.582 | 0.281 | 0.813 | 0.9 | 4.08 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3OXN | 1.52 | 54.284 | 1.41 | 31124 | 1871 | 96.95 | 0.1682 | 0.1665 | 0.1932 |
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 | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 11.527 |
f_angle_d | 1.053 |
f_chiral_restr | 0.061 |
f_bond_d | 0.01 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1551 |
Nucleic Acid Atoms | |
Solvent Atoms | 180 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
DIALS | data reduction |
XSCALE | data scaling |
PHASER | phasing |