3DKO
Complex between the kinase domain of human ephrin type-a receptor 7 (epha7) and inhibitor alw-ii-49-7
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2REI | PDB ENTRY 2REI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 298 | WELL SOLUTION: 25% PEG 3350, 0.1 M NH4 SULPHATE, 0.1 M HEPES PH 7.5. PROTEIN SOLUTION: 15 MG/ML. DROPS: 1:1 RATIO OF WELL:PROTEIN SOLUTION. CRYSTALS CRYOPROTECTED BY TRANSFER TO DROP CONTAINING MOTHER LIQUOR TO WHICH MPD WAS ADDED TO 25%, , pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.42 | 49.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.658 | α = 90 |
b = 52.658 | β = 90 |
c = 217.059 | γ = 120 |
Symmetry | |
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Space Group | P 65 |
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 | 2008-06-20 | 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 | 25 | 95.4 | 0.067 | 38.92 | 9.9 | 21903 | 21903 | -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 | 2.07 | 98.1 | 0.417 | 4.19 | 6.5 | 2253 |
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 | PDB ENTRY 2REI | 2 | 23.69 | 21809 | 20747 | 1062 | 95.3 | 0.19118 | 0.18917 | 0.2316 | RANDOM | 27.811 |
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] | |
1.06 | 0.53 | 1.06 | -1.59 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.222 |
r_dihedral_angle_4_deg | 20.531 |
r_dihedral_angle_3_deg | 12.401 |
r_dihedral_angle_1_deg | 5.13 |
r_scangle_it | 2.329 |
r_scbond_it | 1.451 |
r_angle_refined_deg | 1.156 |
r_mcangle_it | 0.939 |
r_mcbond_it | 0.599 |
r_nbtor_refined | 0.3 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2172 |
Nucleic Acid Atoms | |
Solvent Atoms | 156 |
Heterogen Atoms | 30 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
SBC-Collect | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |