3H9Z
Crystal structure of the IgE-Fc3-4 domains
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1FP5 | PDB entry 1FP5 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.3 | 293 | 1 microliter of protein at 10 mg/mL in 20 mM sodium chloride was added to 1 microliter of well solution (100 mM ammonium acetate, 100 mM sodium acetate pH 4.6, 30% (w/v) PEG 4000) and mixed by pipetting., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51.18 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 65.66 | α = 90 |
b = 99.352 | β = 97.4 |
c = 77.639 | 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 | 113 | CCD | MAR CCD 130 mm | 1999-08-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 5ID-B | 1.0001 | APS | 5ID-B |
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 | 2.45 | 30 | 98.2 | 0.059 | 18.425 | 3.63 | 36017 | 36017 |
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) | |||||||||||
1 | 2.45 | 2.54 | 82.3 | 0.241 | 2.28 |
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 1FP5 | 2.45 | 28.71 | 35946 | 35946 | 1824 | 98.75 | 0.23182 | 0.22936 | 0.27748 | RANDOM | 31.781 |
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] | |
0.57 | 0.21 | 0.55 | -1.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28 |
r_dihedral_angle_4_deg | 15.758 |
r_dihedral_angle_3_deg | 14.975 |
r_dihedral_angle_1_deg | 6.204 |
r_mcangle_it | 2.569 |
r_scangle_it | 2.179 |
r_mcbond_it | 1.522 |
r_angle_refined_deg | 1.448 |
r_scbond_it | 1.396 |
r_angle_other_deg | 0.746 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6624 |
Nucleic Acid Atoms | |
Solvent Atoms | 146 |
Heterogen Atoms | 184 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALEPACK | data scaling |
CNS | refinement |
DENZO | data reduction |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
CNS | phasing |