2DZS
Structure of mutant tryptophan synthase alpha-subunit (E103A) from a hyperthermophile, Pyrococcus furiosus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1GEQ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 283 | 0.1M MES-NAOH, 10-15% PEG 20000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.16 | 43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.283 | α = 90 |
b = 77.688 | β = 90 |
c = 166.687 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | MAR CCD 165 mm | mirror | 2001-05-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 1.0 | SPring-8 | BL41XU |
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 | 2.2 | 99 | 93.9 | 0.047 | 46.9 | 6.05 | 23093 | 23093 | 33.7 |
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) | |||||||||||
2.2 | 2.28 | 69.9 | 0.185 | 6.7 | 6.05 | 1687 |
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 | 1GEQ | 2.4 | 19.7 | 18466 | 18466 | 911 | 97.3 | 0.215 | 0.215 | 0.26 | RANDOM | 30.3 |
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] | |
1.58 | -0.78 | -0.8 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 21.8 |
c_scangle_it | 2.79 |
c_mcangle_it | 2.12 |
c_scbond_it | 1.92 |
c_angle_deg | 1.3 |
c_mcbond_it | 1.3 |
c_improper_angle_d | 0.72 |
c_bond_d | 0.007 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3829 |
Nucleic Acid Atoms | |
Solvent Atoms | 368 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
MAR345dtb | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CNS | phasing |