3P9I
Crystal structure of perennial ryegrass LpOMT1 complexed with S-adenosyl-L-homocysteine and sinapaldehyde
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3P9C | PDB ENTRY 3P9C |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 277 | 0.1 M sodium succinate, 28% (w/v) PEG monomethylether 5000, 2 mM dithiothreitol, 2.5 mM S-adenosyl-L-homocysteine, 5 mM sinapaldehyde, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.23 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 94.938 | α = 90 |
b = 85.225 | β = 111.1 |
c = 98.568 | 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 | CCD | ADSC QUANTUM 315 | mirrors | 2008-11-08 | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.2 | 1.0 | ALS | 8.2.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.85 | 47.071 | 95.7 | 0.085 | 7.3 | 3.1 | 139446 |
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) | ||||||||||
1.85 | 1.95 | 91.4 | 0.367 | 0.367 | 1.7 | 2.4 | 16596 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 3P9C | 1.85 | 47.07 | 139446 | 6972 | 94.4 | 0.2318 | 0.2609 | random | 28.3449 |
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] | |
-14.076 | -0.245 | 14.921 | -0.845 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_scangle_it | 5.515 |
c_scbond_it | 4.212 |
c_mcangle_it | 3.764 |
c_mcbond_it | 2.883 |
c_angle_d | 1.194 |
c_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10760 |
Nucleic Acid Atoms | |
Solvent Atoms | 770 |
Heterogen Atoms | 196 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
SCALA | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
BOS | data collection |
MOSFLM | data reduction |