5X6M
Crystal Structure of SMAD5-MH1 in complex with a composite DNA sequence
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3KMP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | 0.1M Bis-tris, pH 6.5, 0.2M LiNO3, 8% PEG 3350, 5% glycerol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.98 | 69.11 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 119.464 | α = 90 |
b = 119.464 | β = 90 |
c = 93.067 | γ = 120 |
Symmetry | |
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Space Group | P 31 |
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 | 2014-11-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL17U | 0.979065 | SSRF | BL17U |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | 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 | 3.2 | 40 | 98.8 | 0.095 | 0.046 | 22.11 | 5.5 | 24244 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 3.2 | 3.31 | 100 | 0.556 | 0.257 | 0.929 | 4.55 | 5.7 |
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 | FREE R-VALUE | 3KMP | 3.2 | 29.937 | 1.96 | 24146 | 1234 | 98.68 | 0.2125 | 0.2105 | 0.2526 | Random | 125.1 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 23.136 |
f_angle_d | 1.231 |
f_chiral_restr | 0.069 |
f_bond_d | 0.011 |
f_plane_restr | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3575 |
Nucleic Acid Atoms | 1804 |
Solvent Atoms | |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-2000 | data collection |
HKL-2000 | data scaling |
PHASER | phasing |