1B0W
Structural comparison of amyloidogenic light chain dimer in two crystal forms with nonamyloidogenic counterparts
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1BRE | PDB ENTRY 1BRE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | CRYSTALS OF BRE (20MG/ML IN 0.1M TRIS BUFFER, PH 7) WERE GROWN AT RT IN HANGING-DROPS USING 2.5M AMMONIUM SULFATE IN 0.1M CITRATE BUFFER (PH 5.5)., pH 6.5, VAPOR DIFFUSION, HANGING DROP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.2 | 61.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 82.04 | α = 90 |
b = 142.11 | β = 90 |
c = 77.86 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | 287 | IMAGE PLATE | RIGAKU | COLLIMATOR | 1994-02-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.75 | 52.5 | 76 | 0.071 | 0.047 | 7.5 | 2.3 | 35142 | 1 | 17.7 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1.75 | 2 | 56 | 0.218 | 0.255 | 1.92 | 1.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1BRE | 1.8 | 5 | 2 | 31772 | 1568 | 77.3 | 0.226 | 0.299 | RANDOM | 25.3 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 26.9 |
x_angle_deg | 1.84 |
x_improper_angle_d | 1.5 |
x_bond_d | 0.011 |
x_bond_d_na | |
x_bond_d_prot | |
x_angle_d | |
x_angle_d_na | |
x_angle_d_prot | |
x_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2520 |
Nucleic Acid Atoms | |
Solvent Atoms | 104 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
bioteX | data collection |
bioteX | data reduction |
AMoRE | phasing |
X-PLOR | refinement |
bioteX | data scaling |