6PII
The evolving story of AtzT, a periplasmic binding protein
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | Protein at 20 mg/mL in SD2 plates incubated at 20 C. Conditions contained 6-8% Jeffamine M600 with 2-7% MPD and trisodium citrate at 1.1-1.2 M |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.58 | 52.24 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 98.92 | ¦Á = 90 |
b = 63.05 | ¦Â = 93.49 |
c = 120.436 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 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 EIGER X 16M | 2018-09-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 1.008020 | Australian Synchrotron | MX2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.87 | 49.4 | 97.8 | 0.14 | 0.032 | 0.998 | 13.5 | 19.6 | 119947 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.87 | 1.9 | 80.1 | 0.669 | 0.246 | 0.809 | 3.1 | 7.4 |
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 | 1.87 | 49.4 | 114140 | 5791 | 97.59 | 0.15624 | 0.15486 | 0.18303 | RANDOM | 32.759 |
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] | |
1.68 | 2.47 | -2 | 0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.018 |
r_dihedral_angle_3_deg | 14.805 |
r_dihedral_angle_4_deg | 11.229 |
r_long_range_B_refined | 7.089 |
r_long_range_B_other | 7.076 |
r_scangle_other | 6.599 |
r_dihedral_angle_1_deg | 5.822 |
r_scbond_it | 4.435 |
r_scbond_other | 4.405 |
r_mcangle_it | 3.698 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10065 |
Nucleic Acid Atoms | |
Solvent Atoms | 648 |
Heterogen Atoms | 67 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
ADDREF | data reduction |
Aimless | data scaling |
CRANK2 | phasing |