4A0M
CRYSTAL STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE FROM SPINACH IN COMPLEX WITH NAD
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3FG0 | PDB ENTRY 3FG0 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8.5 | CRYSTALS WERE GROWN IN 0.085 M TRIS HYDROCHLORIDE PH 8.5, 0.17 M SODIUM ACETATE TRIHYDRATE, 25.5% W/V POLYETHYLENE GLYCOL 4,000, 15% V/V GLYCEROL. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 41.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 69.406 | α = 79.06 |
b = 80.979 | β = 84.94 |
c = 85.54 | γ = 77.99 |
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 | ADSC CCD | DOUBLE CRYSTAL CHANNEL CUT, SI(III) 1M LONG | 2009-11-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X6A | NSLS | X6A |
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 | 2.3 | 30 | 93.2 | 0.04 | 14.5 | 2.28 | 76619 |
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) | |||||||||||
1 | 2.3 | 2.43 | 81.1 | 0.38 | 2.56 | 2.22 |
Refinement
Statistics | |||||||||||||||||||
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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 | PDB ENTRY 3FG0 | 2.3 | 29.078 | 1.97 | 76619 | 3838 | 96.59 | 0.2343 | 0.2131 | 0.2467 |
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] | |
-1.8302 | 2.4863 | -1.5381 | -2.3988 | -0.0967 | 0.6802 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 20.166 |
f_angle_d | 1.448 |
f_chiral_restr | 0.08 |
f_plane_restr | 0.021 |
f_bond_d | 0.014 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15212 |
Nucleic Acid Atoms | |
Solvent Atoms | 524 |
Heterogen Atoms | 226 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |