5DFV
CRYSTAL STRUCTURE OF HUMAN CD81 LARGE EXTRACELLULAR LOOP IN COMPLEX WITH MURINE FAB FRAGMENT K04
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4 | 293 | 0.1 M NaOAc, 20% PEG 10000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.86 | 56.96 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.631 | α = 90 |
b = 94.483 | β = 104.14 |
c = 94.114 | 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 | CCD | ADSC QUANTUM 315 | 2009-02-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL7-1 | 0.97946 | SSRL | BL7-1 |
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 | 2.8 | 50 | 94 | 0.125 | 7.1 | 3.4 | 30682 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.8 | 2.93 | 63.7 | 0.442 | 1.4 | 1.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | 2.8 | 47.25 | 29086 | 1583 | 93.98 | 0.24213 | 0.23947 | 0.29066 | RANDOM | 29.375 |
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] | |
0.11 | -0.64 | -0.07 | -0.35 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.818 |
r_dihedral_angle_4_deg | 19.023 |
r_dihedral_angle_3_deg | 17.532 |
r_dihedral_angle_1_deg | 6.084 |
r_angle_refined_deg | 1.052 |
r_angle_other_deg | 0.785 |
r_scangle_it | 0.677 |
r_scbond_it | 0.413 |
r_mcangle_it | 0.404 |
r_mcbond_it | 0.365 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7936 |
Nucleic Acid Atoms | |
Solvent Atoms | 5 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALEPACK | data scaling |
DENZO | data reduction |
PHASER | phasing |