3DVI
Crystal structure of kappa 1 amyloidogenic light chain variable domain
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.4 | 295 | Protein: 1.26 mM. Mother Liquor: 15% w/v polyethylene glycol 8000, 0.05 M magnesium acetate, 0.1 M sodium acetate, 0.1 M Tris buffer, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.44 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 47.02 | α = 90 |
b = 47.02 | β = 90 |
c = 103.356 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 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 | IMAGE PLATE | RIGAKU RAXIS IV++ | Osmic VariMax optics | 2007-11-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5241 |
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 | 1.53 | 103.14 | 91 | 0.072 | 20.6 | 16.62 | 18394 | 16734 |
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) | |||||||||||
1.53 | 1.58 | 35.7 | 0.365 | 4.3 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 2Q20 | 1.53 | 103.14 | 18394 | 16194 | 534 | 91.11 | 0.19138 | 0.19138 | 0.18949 | 0.25144 | RANDOM | 18.622 |
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] | |
-0.4 | -0.4 | 0.8 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.39 |
r_dihedral_angle_4_deg | 17.859 |
r_dihedral_angle_3_deg | 14.452 |
r_sphericity_free | 9.015 |
r_dihedral_angle_1_deg | 7.148 |
r_scangle_it | 4.76 |
r_sphericity_bonded | 4.064 |
r_scbond_it | 3.605 |
r_mcangle_it | 2.529 |
r_rigid_bond_restr | 2.128 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 916 |
Nucleic Acid Atoms | |
Solvent Atoms | 202 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrystalClear | data collection |
CrystalClear | data reduction |
CrystalClear | data scaling |
PHASER | phasing |