6OS6
Crystal structure of CymD prenyltransferase complexed with L-tryptophan and DMSPP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5JXM | Author used SWISS-MODEL server to generate a phasing model based on the protein sequence. SWISS-MODEL produced a phasing model based on PDB Entry 5JXM. Author used the polyALA version of the model for phasing. |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 294 | 1% (w/v) tryptone, 0.05 M HEPES-Na (pH 7.0), 12% PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.62 | 53.13 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 129.446 | ¦Á = 90 |
b = 129.446 | ¦Â = 90 |
c = 49.777 | ¦Ã = 90 |
Symmetry | |
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Space Group | I 4 |
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 | 2019-03-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 17-ID-2 | 0.97932 | NSLS-II | 17-ID-2 |
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 | 1.33 | 29.12 | 99.8 | 0.07 | 0.075 | 0.027 | 0.999 | 15 | 7.5 | 95021 | 13.86 |
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 | 1.33 | 1.36 | 97.3 | 0.685 | 0.739 | 0.275 | 0.806 | 7 |
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 | THROUGHOUT | Author used SWISS-MODEL server to generate a phasing model based on the protein sequence. SWISS-MODEL produced a phasing model based on PDB Entry 5JXM. Author used the polyALA version of the model for phasing. | 1.33 | 29.118 | 1.36 | 95019 | 1993 | 99.81 | 0.1665 | 0.1662 | 0.1809 | 18.9029 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2772 |
Nucleic Acid Atoms | |
Solvent Atoms | 411 |
Heterogen Atoms | 66 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |