3H8M
SAM domain of human ephrin type-a receptor 7 (EPHA7)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1B4F |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293.1 | WELL SOLUTION: 20% PEG 4000, 0.2 M SODIUM ACETATE, 0.1 M TRIS HCL PH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.1K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.043553 | 39.810699 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.071 | α = 90 |
b = 54.089 | β = 104.84 |
c = 40.455 | 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 | 2009-04-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E SUPERBRIGHT | 1.54178 |
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 | 2.1 | 22.24 | 97.4 | 0.05 | 25.4 | 3.2 | 9717 | 9717 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
2.1 | 2.18 | 81.1 | 0.315 | 2.59 | 2.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1B4F | 2.1 | 22.24 | 9717 | 9162 | 458 | 97.73 | 0.19867 | 0.19708 | 0.22767 | RANDOM | 20.025 |
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] | |
0.13 | -1.49 | -1.82 | 0.92 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.899 |
r_dihedral_angle_4_deg | 19.234 |
r_dihedral_angle_3_deg | 16.278 |
r_dihedral_angle_1_deg | 4.632 |
r_scangle_it | 3.137 |
r_scbond_it | 1.946 |
r_angle_refined_deg | 1.245 |
r_mcangle_it | 0.989 |
r_mcbond_it | 0.492 |
r_chiral_restr | 0.074 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1174 |
Nucleic Acid Atoms | |
Solvent Atoms | 55 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
SBC-Collect | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |