8SAM
Crystal structure of class III lanthipeptide synthetase LP-GS-ThurKC in complex with ATP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 282.15 | 0.2 M potassium citrate tribasic monohydrate and 19 % w/v PEG 3350, protein incubated at 18 mg/mL with 3mM ATP and 3mM Magnesium Chloride and soaked for 6 hours with 7 mM ATP and 7 mM Calcium Chloride |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.5 | 50.73 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.025 | α = 90 |
b = 228.659 | β = 100.504 |
c = 84.595 | γ = 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 9M | 2021-06-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.00798 | APS | 21-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 2.15 | 49.005 | 86.6 | 0.091 | 0.103 | 0.998 | 9.1 | 4.1 | 94386 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.15 | 2.157 | 82.6 | 1.372 | 1.555 | 0.376 | 0.9 | 4.1 |
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 (All) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.15 | 49.005 | 94248 | 4665 | 86.441 | 0.205 | 0.203 | 0.2505 | 60.008 |
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] | |
-0.855 | -0.701 | 3.844 | -2.553 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.094 |
r_dihedral_angle_4_deg | 19.509 |
r_dihedral_angle_3_deg | 15.202 |
r_lrange_it | 9.302 |
r_dihedral_angle_1_deg | 6.808 |
r_scangle_it | 6.668 |
r_mcangle_it | 5.991 |
r_scbond_it | 4.614 |
r_mcbond_it | 3.969 |
r_angle_refined_deg | 1.192 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13860 |
Nucleic Acid Atoms | |
Solvent Atoms | 405 |
Heterogen Atoms | 64 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
autoPROC | data reduction |
autoPROC | data scaling |
CRANK2 | phasing |