7BIZ
Structure of a B12 binding lipoprotein from Bacteroides thetaiotaomicron
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 293 | Molecular dimensions. Morpheus condition B1 (0.1M Halogens (NaF, NaBr and NaI) 0.1M imidazole, 0.1 MES monohydrate acid pH6.5 and 30% precipitant mix 1 (40% v/v PEG500 MME, 20%W/V PEG 20000)) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.84 | 56.76 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 128.052 | α = 90 |
b = 128.052 | β = 90 |
c = 135.051 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 | PIXEL | DECTRIS PILATUS3 6M | 2019-09-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.96864 | Diamond | I24 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | 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 | 85.74 | 100 | 0.99 | 0.9 | 10.8 | 191916 | 20.85 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.53 | 1.58 | 0.582 |
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-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | In-house structure | 1.53 | 85.7 | 0.03 | 191893 | 9275 | 99.94 | 0.1662 | 0.1649 | 0.1916 | 30.51 |
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 | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 19.6517 |
f_angle_d | 1.5158 |
f_chiral_restr | 0.1478 |
f_bond_d | 0.0089 |
f_plane_restr | 0.0063 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7449 |
Nucleic Acid Atoms | |
Solvent Atoms | 1405 |
Heterogen Atoms | 247 |
Software
Software | |
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Software Name | Purpose |
DIALS | data processing |
Aimless | data scaling |
PHASER | phasing |
Coot | model building |
PHENIX | refinement |
DIALS | data reduction |