3IE5
Crystal structure of Hyp-1 protein from Hypericum perforatum (St John's wort) involved in hypericin biosynthesis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1XDF | PDB ENTRIES 1XDF+2QIM+2FLH+1TW0+2BK0 |
experimental model | PDB | 2QIM | PDB ENTRIES 1XDF+2QIM+2FLH+1TW0+2BK0 |
experimental model | PDB | 2FLH | PDB ENTRIES 1XDF+2QIM+2FLH+1TW0+2BK0 |
experimental model | PDB | 1TW0 | PDB ENTRIES 1XDF+2QIM+2FLH+1TW0+2BK0 |
experimental model | PDB | 2BK0 | PDB ENTRIES 1XDF+2QIM+2FLH+1TW0+2BK0 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 292 | 0.4M NaCl, 0.1M Tris/HCl, 30% (w/v) PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 47.25 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 37.538 | α = 90 |
b = 76.713 | β = 90 |
c = 119.799 | 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 | CCD | MARMOSAIC 225 mm CCD | mirrors | 2008-02-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.91841 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.688 | 30 | 100 | 0.078 | 21.4 | 7 | 39813 | 39813 | -3 | 20.58 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.688 | 1.75 | 99.9 | 0.66 | 2.2 | 5.4 | 3912 |
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 | R-free | PDB ENTRIES 1XDF+2QIM+2FLH+1TW0+2BK0 | 1.688 | 27.663 | 1.34 | 39742 | 39742 | 1590 | 99.89 | 0.172 | 0.172 | 0.17 | 0.206 | random | 27.532 |
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] | |
4.8754 | 4.6346 | -9.51 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 18.846 |
f_angle_d | 1.525 |
f_chiral_restr | 0.11 |
f_bond_d | 0.015 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2737 |
Nucleic Acid Atoms | |
Solvent Atoms | 258 |
Heterogen Atoms | 140 |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
PHASER | phasing |
PHENIX | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |