4DUV
E. coli (lacZ) beta-galactosidase (G974A) 2-deoxy-galactosyl-enzyme and bis-Tris complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1JYX |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 288 | 10% PEG 8000, 100 MM BIS-TRIS, 200 MM MGCL2, 100 MM NACL, 10 MM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.66 | 53.72 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 150.57 | α = 90 |
b = 167.731 | β = 90 |
c = 201.64 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 315 | 2007-08-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08B1-1 | 1.11589 | CLSI | 08B1-1 |
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 | 2.1 | 200 | 100 | 0.11 | 12.7 | 7.6 | 295878 | 295878 |
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 | 2.1 | 2.21 | 100 | 0.482 | 3.8 | 7.6 |
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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | 1JYX | 2.1 | 86.41 | 291478 | 291478 | 4267 | 100 | 0.15911 | 0.15843 | 0.2064 | RANDOM | 31.263 |
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] | |
-0.44 | 1.68 | -1.24 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.755 |
r_dihedral_angle_4_deg | 14.719 |
r_dihedral_angle_3_deg | 12.599 |
r_dihedral_angle_1_deg | 6.141 |
r_scangle_it | 5.843 |
r_scbond_it | 4.335 |
r_mcangle_it | 2.971 |
r_mcbond_it | 2.052 |
r_angle_refined_deg | 1.064 |
r_chiral_restr | 0.072 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 32732 |
Nucleic Acid Atoms | |
Solvent Atoms | 4018 |
Heterogen Atoms | 481 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CNS | refinement |
ADSC | data collection |
MOSFLM | data reduction |
SCALA | data scaling |
CNS | phasing |