3HK0
Crystal Structure of the RA and PH Domains of Grb10
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 310 | crystals were grown at 17 C in hanging drops containing equal volumes of protein solution and reservoir buffer (~15% PEG 3350, 0.15 M sodium thiocyanate, and 1 mM dithiothreitol (DTT)), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 310K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.21 | 44.38 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 126.875 | α = 90 |
b = 48.884 | β = 114.14 |
c = 92.217 | 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 | CCD | ADSC QUANTUM 4 | 2007-09-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4A | 0.9798 | NSLS | X4A |
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 | 2.6 | 30 | 99.6 | 0.062 | 0.062 | 13.8 | 3.8 | 16167 | 2 | 2 |
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 | 2.6 | 2.667 | 99.4 | 0.323 | 0.323 | 3 | 3.5 |
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 | SAD | THROUGHOUT | 2.6 | 30 | 15264 | 821 | 99.59 | 0.23221 | 0.22972 | 0.27689 | RANDOM | 46.91 |
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] | |
-0.1 | -0.62 | 1.26 | -1.66 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.935 |
r_dihedral_angle_4_deg | 18.279 |
r_dihedral_angle_3_deg | 18.158 |
r_dihedral_angle_1_deg | 5.46 |
r_scangle_it | 1.07 |
r_angle_refined_deg | 1.059 |
r_scbond_it | 0.649 |
r_mcangle_it | 0.493 |
r_nbtor_refined | 0.297 |
r_mcbond_it | 0.259 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3525 |
Nucleic Acid Atoms | |
Solvent Atoms | 14 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
SOLVE | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |