3SYX
Crystal Structure of the WH1 domain from human sprouty-related, EVH1 domain-containing protein. Northeast Structural Genomics Consortium Target HR5538B.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | Microbatch crystallization under oil | 6 | 277 | 12% PEG 20000, 0.1 M potassium acetate, 10 mM yttrium(III) chloride, 0.1 M MES, pH 6.0, Microbatch crystallization under oil, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.29 | 62.67 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.754 | α = 90 |
b = 52.754 | β = 90 |
c = 121.638 | γ = 120 |
Symmetry | |
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Space Group | P 31 1 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 | 100 | CCD | ADSC QUANTUM 4 | 2011-07-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4A | 0.97896 | NSLS | X4A |
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 | 2.45 | 50 | 99.7 | 0.057 | 29.6 | 4.9 | 27822 | 27739 | 55.94 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.45 | 2.54 | 99.9 | 0.691 | 2.5 | 4.5 | 2826 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | pdb entry 1XOD | 2.453 | 26.377 | 1.03 | 13821 | 650 | 99.54 | 0.23 | 0.228 | 0.271 | RANDOM | 63.317 |
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] | |
3.896 | 3.896 | -7.791 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.719 |
f_angle_d | 1.664 |
f_chiral_restr | 0.12 |
f_bond_d | 0.009 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 933 |
Nucleic Acid Atoms | |
Solvent Atoms | 21 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
BALBES | phasing |