2JA4
Crystal structure of CD5 domain III reveals the fold of a group B scavenger cysteine-rich receptor
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.4 | 15-25% PEG 8000, 100 MM NAAC PH 4.4, 200 MM LI2SO4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.7 | 67.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.931 | α = 90 |
b = 62.931 | β = 90 |
c = 72.564 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 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 | MARRESEARCH | 2006-06-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | SLS | X06SA |
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 | 2.21 | 50 | 96.9 | 0.05 | 15.3 | 5.4 | 12098 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.21 | 2.26 | 95.6 | 0.24 | 2.2 | 4.1 |
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 | SAD | THROUGHOUT | 2.21 | 19.18 | 7899 | 387 | 95.6 | 0.196 | 0.193 | 0.248 | RANDOM | 44.77 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.38 | 0.19 | 0.38 | -0.57 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.047 |
r_dihedral_angle_4_deg | 25.84 |
r_dihedral_angle_3_deg | 19.026 |
r_dihedral_angle_1_deg | 12.584 |
r_scangle_it | 9.823 |
r_scbond_it | 7.241 |
r_mcangle_it | 4.863 |
r_mcbond_it | 3.492 |
r_angle_refined_deg | 2.156 |
r_nbtor_refined | 0.33 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 789 |
Nucleic Acid Atoms | |
Solvent Atoms | 58 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
ARP/wARP | model building |
SCALEPACK | data scaling |
BNP | phasing |
SHARP | phasing |
SOLOMON | phasing |
ARP/wARP | phasing |
REFMAC | refinement |