3ACO
Crystal structure of the EFC/F-BAR domain of human PACSIN2/Syndapin II (2.7 A)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 10% PEG 3350, 0.1M calcium chloride, 0.03M glycyl-glycyl-glycine, 0.05 M Tris-HCl, 0.075M NaCl, 0.001M DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.91 | 57.77 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 31.607 | α = 90 |
b = 84.654 | β = 90 |
c = 357.335 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | mirrors | 2009-01-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 0.97920 | Photon Factory | BL-5A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.7 | 50 | 97.6 | 0.164 | 14.3 | 9.5 | 27264 | -3 | 59.1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.7 | 2.8 | 90.9 | 0.395 | 5.1 | 8.6 | 2445 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.7 | 39.88 | 26723 | 26723 | 1303 | 96.2 | 0.226 | 0.226 | 0.279 | RANDOM | 65.2 |
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] | |
-5.31 | -2.36 | 7.68 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_scangle_it | 20.31 |
c_dihedral_angle_d | 18 |
c_mcangle_it | 16.3 |
c_scbond_it | 13.96 |
c_mcbond_it | 10.45 |
c_angle_deg | 1 |
c_improper_angle_d | 0.65 |
c_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4708 |
Nucleic Acid Atoms | |
Solvent Atoms | 273 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
SnB | phasing |
CNS | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |