3O2K
Crystal Structure of Brevianamide F Prenyltransferase Complexed with Brevianamide F and Dimethylallyl S-thiolodiphosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3O24 | PDB ENTRY 3O24 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 298 | 1.3M ammonium sulfate, 0.2M lithium sulfate, 0.1M MES, VAPOR DIFFUSION, HANGING DROP. Stepwise transferred to 1.3M lithium sulfate, 0.1M MES pH 6.5, 2.5mM brevianamide F, 10mM dimethylallyl S-thiolodiphosphate for soaking, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.97 | 37.7 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 82.77 | ¦Á = 90 |
b = 82.77 | ¦Â = 90 |
c = 124.26 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 | PSI PILATUS 6M | 2009-12-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.0000 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | 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 | 2.4 | 30 | 99.9 | 0.042 | 0.109 | 29.95 | 23.6 | 17531 | 17518 | 3 | 3 | 50.1 |
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) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.4 | 2.46 | 100 | 0.228 | 0.407 | 8.61 | 27 | 1258 |
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 (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 3O24 | 2.4 | 20 | 3 | 17531 | 16613 | 874 | 100 | 0.209 | 0.20681 | 0.20534 | 0.23451 | imported from native structure, random extension to full resolution | 58.076 |
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] | |
-4.51 | -4.51 | 9.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.18 |
r_dihedral_angle_4_deg | 14.209 |
r_dihedral_angle_3_deg | 12.024 |
r_dihedral_angle_1_deg | 4.73 |
r_scangle_it | 1.498 |
r_mcangle_it | 1.051 |
r_scbond_it | 0.974 |
r_angle_refined_deg | 0.825 |
r_angle_other_deg | 0.746 |
r_mcbond_it | 0.597 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3393 |
Nucleic Acid Atoms | |
Solvent Atoms | 46 |
Heterogen Atoms | 49 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
REFMAC | phasing |