4LID
A100, A DNA binding scaffold from Sulfolobus spindle-shape virus 1
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 296 | 10mg/ml A100, 0.6-0.9M Ammonium dihydrogen phosphate, 20-30% Glycerol, 0.7M MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
2 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 296 | 10mg/ml selenomethionine incorporated A100,0.6-0.9M Ammonium dihydrogen phosphate, 20-30% Glycerol, 0.7M MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 152.999 | α = 90 |
b = 152.999 | β = 90 |
c = 61.727 | γ = 120 |
Symmetry | |
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Space Group | P 63 2 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 | 102.5 | PIXEL | DECTRIS PILATUS 6M | K-B focusing mirrors | 2013-04-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 0.9795 | SSRL | BL12-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | 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 | 3 | 38.25 | 99.9 | 0.014 | 0.047 | 7.93 | 12.5 | 8956 | 8953 | 2 | 1 | 94.1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3 | 3.16 | 100 | 0.688 | 0.2 | 5.2 | 12.5 | 1263 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | 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 | SAD | THROUGHOUT | 3 | 21 | 2 | 8957 | 8488 | 423 | 99.5 | 0.2857 | 0.23767 | 0.23707 | 0.25062 | RANDOM | 122.806 |
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] | |
0.25 | 0.25 | 0.25 | -0.8 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.516 |
r_dihedral_angle_3_deg | 16.32 |
r_dihedral_angle_4_deg | 9.045 |
r_dihedral_angle_1_deg | 6.546 |
r_angle_other_deg | 2.96 |
r_angle_refined_deg | 1.743 |
r_chiral_restr | 0.083 |
r_bond_refined_d | 0.015 |
r_gen_planes_refined | 0.006 |
r_gen_planes_other | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1438 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHENIX | model building |
REFMAC | refinement |
autoXDS | data reduction |
SCALA | data scaling |
PHENIX | phasing |