4W6Z
YEAST ALCOHOL DEHYDROGENASE I, SACCHAROMYCES CEREVISIAE FERMENTATIVE ENZYME
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1LLU | 1LLU.PDB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.4 | 278 | 125 MM SODIUM N-TRIS(HYDROXYMETHYL) METHYL-3-AMINOPROPANE SULFONIC ACID, 1.7 MM NICOTINAMIDE 8- IODOADENINE DINUCLEOTIDE, 0.1 M 2,2,2-TRIFLUOROETHANOL, 0.16 MM EDTA, 10 MG/ML PROTEIN, 6% INITIAL POLYETHYLENE GLYCOL 5000 MONOMETHYL ETHER (FLUKA MPEG5000) IN DROP HANGING OVER 22-26% MPEG5000 AND 0.1 M 2,2,2-TRIFLUOROETHANOL. CRYSTALS WERE SOAKED IN SAME BUFFER WITH 30% W/V MPEG5000 WITH 0.5 M 2,2,2- TRIFLUOROETHANOL FOR FIVE DAYS BEFORE FREEZING AT 100 K., PH 8.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 278K, PH 8.40 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.62 | 53.07 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 144.338 | ¦Á = 90 |
b = 144.338 | ¦Â = 90 |
c = 128.204 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 3 2 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 | IMAGE PLATE | MAR scanner 300 mm plate | MULTIPOLE WIGGLER | 1995-07-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7A | 0.857 | EMBL/DESY, HAMBURG | BW7A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.4 | 40.4 | 98.5 | 0.116 | 0.116 | 8 | 3.85 | 59662 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.4 | 2.49 | 93.3 | 0.418 | 0.418 | 3.5 | 3.71 |
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 | 1LLU.PDB | 2.4 | 28.09 | 58104 | 1473 | 98.54 | 0.17767 | 0.17652 | 0.22177 | RANDOM | 40.195 |
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] | |
-8.39 | -8.39 | 16.79 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.239 |
r_dihedral_angle_4_deg | 22.52 |
r_dihedral_angle_3_deg | 18.884 |
r_dihedral_angle_1_deg | 7.25 |
r_long_range_B_refined | 4.147 |
r_long_range_B_other | 4.126 |
r_mcangle_it | 2.183 |
r_mcangle_other | 2.183 |
r_scangle_other | 2.151 |
r_angle_refined_deg | 1.861 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10328 |
Nucleic Acid Atoms | |
Solvent Atoms | 151 |
Heterogen Atoms | 122 |
Software
Software | |
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Software Name | Purpose |
d*TREK | data scaling |
AMoRE | phasing |
REFMAC | refinement |