6PTL
Structure of the self-association domain of the chromatin looping factor LDB1
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 18.6% PEG3350, 140 mM sodium phosphate dibasic | |
2 | VAPOR DIFFUSION, SITTING DROP | 293 | 18.6% PEG3350, 140 mM sodium phosphate dibasic, crystal soaked overnight in mother liquor containing 10 mM ethylmercury thiosalicylic acid |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.86 | 56.99 |
2.86 | 56.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.869 | α = 90 |
b = 81.869 | β = 90 |
c = 66.828 | γ = 120 |
Symmetry | |
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Space Group | P 32 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 | CCD | ADSC QUANTUM 315r | 2014-09-27 | M | SINGLE WAVELENGTH | ||||||
2 | 2 | x-ray | 100 | CCD | ADSC QUANTUM 210r | 2015-02-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.9537 | Australian Synchrotron | MX2 |
2 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX1 | 0.9537 | Australian Synchrotron | MX1 |
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 | 2.5 | 35.5 | 99.7 | 0.083 | 0.087 | 0.027 | 0.998 | 14.7 | 10.7 | 9212 | 75.2 |
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 | 2.5 | 2.6 | 100 | 1.213 | 1.271 | 0.381 | 0.929 | 2.5 | 11 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2.5 | 35.48 | 8696 | 496 | 99.47 | 0.2463 | 0.2448 | 0.2708 | RANDOM | 87.291 |
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] | |
2.28 | 1.14 | 2.28 | -7.41 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 25.685 |
r_dihedral_angle_4_deg | 18.234 |
r_dihedral_angle_3_deg | 12.752 |
r_dihedral_angle_1_deg | 5.46 |
r_angle_refined_deg | 1.14 |
r_angle_other_deg | 1.013 |
r_chiral_restr | 0.032 |
r_gen_planes_refined | 0.002 |
r_bond_refined_d | 0.001 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1213 |
Nucleic Acid Atoms | |
Solvent Atoms | 9 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |