4NFS
V203A horse liver alcohol dehydrogenase E complexed with NAD and 2,2,2-trifluoroethanol
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4DXH | PDB ENTRY 4DXH |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICRODIALYSIS | 7 | 278 | 50 mN ammonium N-[tris(hydroxymethyl)methyl]-2-amminoethanesulfonate and 0.5 mM EDTA, pH 6.7 (at 25 deg C), 10 mg/ml protein, 1 mM NAD+, 100 mM 2,2,2-trifluoroethanol, 13-25 % 2-methyl-2,4-methylpentanediol, MICRODIALYSIS, temperature 278K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 48.83 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.28 | α = 91.88 |
b = 51.41 | β = 103.09 |
c = 92.53 | γ = 109.94 |
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 | NOIR-1 | Rosenbaum-Rock vertically focussed mirrors | 2007-07-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 4.2.2 | 0.802 | ALS | 4.2.2 |
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 | 1.1 | 20 | 88.3 | 0.041 | 12.2 | 3.05 | 310308 | 266123 | 11.9 |
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 | 1.1 | 1.14 | 50.6 | 0.385 | 2.2 | 2.91 | 15266 |
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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 4DXH | 1.1 | 19.58 | 263388 | 2690 | 88.31 | 0.13781 | 0.13743 | 0.17474 | RANDOM | 17.884 |
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] | |
0.04 | -0.08 | -0.02 | 0.21 | -0.34 | -0.16 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 53.322 |
r_dihedral_angle_2_deg | 38.071 |
r_sphericity_bonded | 13.932 |
r_dihedral_angle_4_deg | 13.355 |
r_rigid_bond_restr | 12.098 |
r_dihedral_angle_3_deg | 11.105 |
r_dihedral_angle_1_deg | 6.256 |
r_long_range_B_refined | 5.868 |
r_long_range_B_other | 4.218 |
r_scangle_other | 3.338 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5566 |
Nucleic Acid Atoms | |
Solvent Atoms | 1034 |
Heterogen Atoms | 136 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |