3E1F
E.Coli (lacZ) beta-galactosidase (H418E) in complex with galactose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1JYX | PDB entry 1JYX |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 288 | Bis-Tris, PEG 8000, MgCl2, NaCl, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 288K, pH 6.50 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.71 | 54.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 128.37 | α = 90 |
b = 152.87 | β = 102.68 |
c = 132.12 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | ADSC QUANTUM 210 | KOHZU: Double Crystal Si (111) | 2007-08-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.11588 | ALS | 8.3.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 3 | 98.54 | 90713 | 90713 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
3 | 90713 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 1JYX | 3 | 98.54 | 99534 | 90712 | 4529 | 91.1 | 0.218 | 0.249 | 1.5%, consistent with previous structures. | 43.38 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
13.08 | -0.54 | -4.42 | -8.66 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
x_torsion_deg | 25.2 |
x_angle_deg | 1.4 |
x_torsion_impr_deg | 0.93 |
x_bond_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 32496 |
Nucleic Acid Atoms | |
Solvent Atoms | 328 |
Heterogen Atoms | 411 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
ADSC | data collection |
MOSFLM | data reduction |
SCALA | data scaling |
CNS | phasing |