4LHP
Crystal Structure of Native FG41Malonate Semialdehyde Decarboxylase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2AAL | PDB ENTRY 2AAL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | Sitting drop | 7.5 | 277 | 3 micro liter of protein solution (20.5 mg/mL in 10 mM sodium phosphate buffer, pH 8) mixed with 3 micro liter crystallization solution (0.1 M HEPES-Na buffer, pH 7.5, 2% v/v polyethylene glycol 400, 2.0 M ammonium sulfate), Sitting drop, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 46.48 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 88.955 | α = 90 |
b = 94.692 | β = 90 |
c = 190.701 | 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 | IMAGE PLATE | RIGAKU RAXIS | 2007-06-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.5418 |
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 | 2 | 50 | 85.8 | 0.154 | 96503 | 91098 | 1.34 | 2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution 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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 2AAL | 2.02 | 40.826 | 1.34 | 95653 | 91098 | 4560 | 85.81 | 0.196 | 0.1936 | 0.2411 | Random |
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 |
f_dihedral_angle_d | 12.742 |
f_angle_d | 0.764 |
f_chiral_restr | 0.043 |
f_bond_d | 0.004 |
f_plane_restr | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11805 |
Nucleic Acid Atoms | |
Solvent Atoms | 1173 |
Heterogen Atoms | 70 |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
CaspR | model building |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CaspR | phasing |