1LNH
LIPOXYGENASE-3(SOYBEAN) NON-HEME FE(II) METALLOPROTEIN
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2SBL | FOR MOLECULAR REPLACEMENT: 1SBL FOR SOYBEAN LIPOXYGENASE-1. THE MODEL WAS TRUNCATED TO INCLUDE ONLY THE ATOMS (7854) COMMON WITH LIPOXYGENASE-3 SEQUENCE (ENTRY 1SBL WAS REPLACED LATER IN PDB BY 2SBL WITH BETTER REFINED MODEL). |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 5.3 | pH 5.3 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.46 | 50 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 112.8 | α = 90 |
b = 137.4 | β = 95.5 |
c = 61.85 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 296 | IMAGE PLATE | RIGAKU | 1994-08-16 | M |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE |
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 | 2.6 | 61.6 | 80.1 | 0.062 | 23403 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
2.6 | 2.75 | 43.6 | 0.117 | 3.39 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution 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 | FOR MOLECULAR REPLACEMENT: 1SBL FOR SOYBEAN LIPOXYGENASE-1. THE MODEL WAS TRUNCATED TO INCLUDE ONLY THE ATOMS (7854) COMMON WITH LIPOXYGENASE-3 SEQUENCE (ENTRY 1SBL WAS REPLACED LATER IN PDB BY 2SBL WITH BETTER REFINED MODEL). | 2.6 | 8 | 2 | 22402 | 82.1 | 0.174 | 0.174 | 0.265 | 31.7 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 25.46 |
x_angle_deg | 3.55 |
x_improper_angle_d | 1.54 |
x_bond_d | 0.015 |
x_bond_d_na | |
x_bond_d_prot | |
x_angle_d | |
x_angle_d_na | |
x_angle_d_prot | |
x_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6696 |
Nucleic Acid Atoms | |
Solvent Atoms | 170 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
X-PLOR | model building |
X-PLOR | refinement |
MSC | data reduction |
X-PLOR | phasing |