5MJ1
Extracellular domain of human CD83 - rhombohedral crystal form
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.2 microliter protein (39 mg/ml in ultrapure water) mixed with 0.4 microliter reservoir solution (0.2 M DL-malic acid (pH 7.0), 20% w/v PEG 3350) was equilibrated against 70 microliter of reservoir solution. Crystals appeared after ~ 13 months |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2 | 38.64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.803 | α = 90 |
b = 62.803 | β = 90 |
c = 134.86 | γ = 120 |
Symmetry | |
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Space Group | H 3 2 |
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 | PIXEL | DECTRIS PILATUS 6M | 2014-03-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.918409 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.8 | 31.4 | 99.8 | 0.053 | 21 | 5.4 | 9772 | 33.7 |
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 | 1.8 | 1.91 | 99.7 | 0.74 | 2.2 | 5.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.8 | 31.4 | 1.36 | 9771 | 489 | 99.81 | 0.1743 | 0.1722 | 0.2156 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 11.445 |
f_angle_d | 1.137 |
f_chiral_restr | 0.043 |
f_bond_d | 0.007 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 616 |
Nucleic Acid Atoms | |
Solvent Atoms | 58 |
Heterogen Atoms | 7 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
MxCuBE | data collection |
XDS | data reduction |
Coot | model building |