8TED
PorX primitive orthorhombic crystal form
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 0.16 M calcium acetate, 0.08 M sodium cacodylate pH 6.5, 14.4% polyethylene glycol 8000 and 20% glycerol, 0.5 M sodium bromide |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.28 | 46.05 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 84.696 | α = 90 |
b = 97.849 | β = 90 |
c = 133.2 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 100 | PIXEL | DECTRIS PILATUS3 6M | 2021-02-17 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08B1-1 | 0.9537 | CLSI | 08B1-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.1 | 46.16 | 99.6 | 0.091 | 0.098 | 0.038 | 0.998 | 13.7 | 6.7 | 65014 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.1 | 2.15 | 99.1 | 0.573 | 0.62 | 0.234 | 0.925 | 6.9 |
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 | MAD | THROUGHOUT | 2.1 | 42.4 | 61660 | 3297 | 99.45 | 0.181 | 0.17863 | 0.22563 | RANDOM | 31.631 |
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] | |
-1.91 | -0.85 | 2.76 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.455 |
r_dihedral_angle_4_deg | 16.238 |
r_dihedral_angle_3_deg | 15.452 |
r_long_range_B_refined | 7.189 |
r_long_range_B_other | 7.126 |
r_dihedral_angle_1_deg | 6.886 |
r_scangle_other | 4.927 |
r_mcangle_it | 3.611 |
r_mcangle_other | 3.61 |
r_scbond_it | 3.182 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8386 |
Nucleic Acid Atoms | |
Solvent Atoms | 686 |
Heterogen Atoms | 33 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data scaling |
XDS | data reduction |
CRANK2 | phasing |