6NKQ
The structure of bovine beta-lactoglobulin in novel crystals grown at pH 3.8
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 3.8 | 293 | Reservoir of 3 M NaCl buffered with sodium citrate at pH 3.8 - heavy white precipitate formed upon mixing of 30 mg/ml protein in water with reservoir solution. Precipitate was removed by centrifugation. The clear remaining 12ul droplet was equilibrated against the reservoir for 12 to 60 hours |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.21 | 44.31 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 65.888 | α = 90 |
b = 114.121 | β = 90 |
c = 140.506 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | 173 | PIXEL | DECTRIS PILATUS 300K | 2018-02-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | .987 | ALS | 8.3.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.2 | 60 | 94 | 0.205 | 0.19 | 0.209 | 0.031 | 0.999 | 10.7 | 45.2 | 49538 | 93 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 2.2 | 2.7 | 45.3 | 1.62 | 1.62 | 1.66 | 0.24 | 0.976 | 3.4 | 46.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1BEB | 2.3 | 57.06 | 43606 | 2327 | 99.46 | 0.20974 | 0.20681 | 0.26097 | RANDOM | 92.982 |
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] | |
110.93 | -1.74 | 18.76 | -129.69 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.383 |
r_long_range_B_refined | 15.927 |
r_long_range_B_other | 15.926 |
r_dihedral_angle_4_deg | 15.919 |
r_dihedral_angle_3_deg | 15.061 |
r_mcangle_it | 11.171 |
r_mcangle_other | 11.17 |
r_scangle_other | 9.357 |
r_mcbond_other | 8.173 |
r_mcbond_it | 8.172 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7519 |
Nucleic Acid Atoms | |
Solvent Atoms | 67 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |