5CDG
I220F horse liver alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4DWV |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICRODIALYSIS | 7 | 278 | 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfonate, 0.25 mM EDTA, pH 6.7 (at 25 C), 1.0 mM NAD+, 10 mM 2,3,4,5,6-pentafluorbenzyl alcohol, 16 to 25 % 2-methyl-2,4-pentanediol, 10 mg/ml protein in dialysis bag. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 48.84 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.26 | α = 91.75 |
b = 51.38 | β = 103.1 |
c = 92.39 | γ = 109.36 |
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 | 2009-01-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 4.2.2 | 0.80 | 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 | 1.4 | 20 | 82.9 | 0.065 | 7.9 | 3.48 | 119994 | 18.3 |
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 | 1.4 | 1.43 | 83.3 | 0.474 | 1.8 | 3.52 |
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 | 4DWV | 1.4 | 20 | 119994 | 1803 | 82.89 | 0.14237 | 0.1417 | 0.18709 | RANDOM | 22.459 |
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] | |
0.2 | 0.29 | -0.08 | 0.74 | 0.18 | -1.18 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.483 |
r_sphericity_free | 24.122 |
r_dihedral_angle_4_deg | 15.51 |
r_dihedral_angle_3_deg | 12.321 |
r_sphericity_bonded | 8.341 |
r_dihedral_angle_1_deg | 6.341 |
r_rigid_bond_restr | 6.243 |
r_long_range_B_refined | 3.921 |
r_long_range_B_other | 3.424 |
r_scangle_other | 3.415 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5576 |
Nucleic Acid Atoms | |
Solvent Atoms | 896 |
Heterogen Atoms | 134 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |
O | model building |
REFMAC | phasing |