1LLU
THE TERNARY COMPLEX OF PSEUDOMONAS AERUGINOSA ALCOHOL DEHYDROGENASE WITH ITS COENZYME AND WEAK SUBSTRATE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1YKF | PDB ENTRY 1YKF |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.6 | 292 | 2mM NAD+, 16mM Spermine, 14% Polyethelene Glycol Monomethyl Ether 2000, 12mM Sodium Potassium Tartrate, 100mM Tris pH 8.6, 0.1mM DTT, 0.007% Sodium Azide, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.58 | 52.35 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 74.171 | ¦Á = 79.34 |
b = 86.328 | ¦Â = 78.66 |
c = 125.698 | ¦Ã = 71.58 |
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 | 120 | IMAGE PLATE | RIGAKU RAXIS IV++ | Osmic-Blue confocal optics | 2001-11-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.3 | 20 | 96.4 | 0.108 | 12.1 | 3.4 | 123136 | 123136 | -3 | 19.5 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.3 | 2.34 | 94.2 | 0.463 | 2.8 | 3.3 | 6019 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1YKF | 2.3 | 19.99 | -3 | 123136 | 123017 | 12264 | 96.4 | 0.229 | 0.246 | RANDOM | 31.3 |
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] | |
4.49 | -4.99 | 0.21 | -0.85 | 2.01 | -3.64 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 24.4 |
c_scangle_it | 2.94 |
c_scbond_it | 1.97 |
c_mcangle_it | 1.94 |
c_angle_deg | 1.5 |
c_improper_angle_d | 1.19 |
c_mcbond_it | 1.19 |
c_bond_d | 0.008 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 20120 |
Nucleic Acid Atoms | |
Solvent Atoms | 1044 |
Heterogen Atoms | 416 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
MOLREP | phasing |
CNS | refinement |