4NFH
V207A Horse Liver Alcohol Dehydrogenase E complexed with NAD and 2,3,4,5,6-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 | PDB ENTRY 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-aminoethane sulfonate, pH 6.7 (at 25 C), 0.25 mM EDTA, 10 mg/ml protein, 1 mM NAD+, 10 mM 2,3,4,5,6-pentafluorobenzyl alcohol, 12 TO 25 % 2-methyl-2,4-pentanediol, MICRODIALYSIS, temperature 278K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 48.67 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 44.49 | ¦Á = 91.96 |
b = 51.23 | ¦Â = 103 |
c = 92.32 | ¦Ã = 110.28 |
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 vertical focussing mirrors | 2008-12-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 4.2.2 | 0.827 | 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 | 1.2 | 20 | 94.2 | 0.055 | 11.3 | 3.77 | 217807 | 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 | 1.2 | 1.24 | 74 | 0.363 | 2.4 | 3.46 | 17131 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 4DWV | 1.2 | 19.84 | 216747 | 1066 | 94.14 | 0.13547 | 0.13547 | 0.13532 | 0.16569 | RANDOM | 16.966 |
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] | |
0.24 | -0.49 | 0.24 | 0.23 | 0.15 | -0.39 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 41.554 |
r_dihedral_angle_2_deg | 38.114 |
r_dihedral_angle_4_deg | 14.701 |
r_dihedral_angle_3_deg | 11.387 |
r_sphericity_bonded | 10.42 |
r_dihedral_angle_1_deg | 6.244 |
r_long_range_B_refined | 5.096 |
r_rigid_bond_restr | 3.921 |
r_long_range_B_other | 3.814 |
r_scangle_other | 3.088 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5566 |
Nucleic Acid Atoms | |
Solvent Atoms | 994 |
Heterogen Atoms | 150 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |