4H6C
Crystal Structure of the Allene Oxide Cyclase 1 from Physcomitrella patens
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2DIO |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.2 | 292 | Hampton Magic Screen condition no. 49 containing 20 % (w/v) PEG 8000, 0.1 M Na3PO4, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51.13 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.321 | α = 84.61 |
b = 67.43 | β = 79.32 |
c = 161.775 | γ = 61.99 |
Symmetry | |
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Space Group | P 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 | MARMOSAIC 225 mm CCD | mirrors | 2008-11-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.9184 | 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 | 1.35 | 19.8 | 82.4 | 0.023 | 15.98 | 1.7 | 446841 | 446841 | -3 | 22.825 |
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 | 1.35 | 1.45 | 79.3 | 0.417 | 2.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2DIO | 1.35 | 19.8 | -3 | 446841 | 424547 | 22345 | 82.39 | 0.1396 | 0.1378 | 0.1741 | thin shells (NCS) | 27.2248 |
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] | |
-0.19 | 0.34 | 0.01 | 0.33 | -0.86 | -0.29 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 32.952 |
r_dihedral_angle_2_deg | 29.59 |
r_sphericity_bonded | 18.593 |
r_dihedral_angle_4_deg | 15.106 |
r_dihedral_angle_3_deg | 11.417 |
r_dihedral_angle_1_deg | 6.258 |
r_rigid_bond_restr | 4.104 |
r_angle_refined_deg | 1.587 |
r_chiral_restr | 0.107 |
r_bond_refined_d | 0.016 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 16577 |
Nucleic Acid Atoms | |
Solvent Atoms | 2591 |
Heterogen Atoms | 133 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
XSCALE | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MAR345dtb | data collection |
XDS | data reduction |
PHASER | phasing |