1YXQ
Crystal structure of actin in complex with swinholide A
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | small-scale batch | 8.5 | 277 | dimethyl PEG 5000, HEPPS, MgCl2, TCEP, NaN3, pH 8.5, small-scale batch, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3 | 58.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68 | α = 90 |
b = 76.8 | β = 101.2 |
c = 98.4 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | IMAGE PLATE | RIGAKU RAXIS IV | 2002-08-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU300 | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.01 | 50 | 99.4 | 0.055 | 24.9 | 3.4 | 66550 | 66151 | 29.4 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.01 | 2.08 | 95.7 | 0.301 | 3.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2.01 | 50 | 63056 | 62779 | 3353 | 99.56 | 0.186 | 0.186 | 0.184 | 0.219 | RANDOM | 23.922 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.39 | 1.87 | -1.05 | 2.16 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 6.12 |
r_scangle_it | 4.43 |
r_scbond_it | 2.926 |
r_mcangle_it | 1.709 |
r_angle_other_deg | 1.672 |
r_angle_refined_deg | 1.648 |
r_mcbond_it | 0.962 |
r_symmetry_vdw_other | 0.357 |
r_symmetry_vdw_refined | 0.305 |
r_symmetry_hbond_refined | 0.295 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5591 |
Nucleic Acid Atoms | |
Solvent Atoms | 282 |
Heterogen Atoms | 171 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
MOLREP | phasing |
REFMAC | refinement |