4EV0
Crystal Structure of Thermus thermophilus Catabolite Activator Protein
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2PQQ | Nterminal domain: composite model of pruned fragments from PDB entries 2pqq, 3d0s, 3h3u representing residues 21-102; C-terminal domain: pruned fragment from PDB entry 2zcw |
experimental model | PDB | 3D0S | Nterminal domain: composite model of pruned fragments from PDB entries 2pqq, 3d0s, 3h3u representing residues 21-102; C-terminal domain: pruned fragment from PDB entry 2zcw |
experimental model | PDB | 3H3U | Nterminal domain: composite model of pruned fragments from PDB entries 2pqq, 3d0s, 3h3u representing residues 21-102; C-terminal domain: pruned fragment from PDB entry 2zcw |
experimental model | PDB | 2ZCW | Nterminal domain: composite model of pruned fragments from PDB entries 2pqq, 3d0s, 3h3u representing residues 21-102; C-terminal domain: pruned fragment from PDB entry 2zcw |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | Screening for crystallization used the Gryphon liquid handling system (Art Robbins Instruments). Crystals were grown using sitting drops (200 nL protein + 200 nL crystallization reagent) with 60 UL reservoirs of crystallization reagent in a 96-well high-throughput screen. Plate-shaped crystals were obtained at 20 degree C using Hampton Research NATRIX HT #38: 0.2 M ammonium acetate, 0.15 M magnesium acetate tetrahydrate, 5% (w/v) polyethylene glycol 4000, and 0.05 M HEPES sodium, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.79 | 55.95 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.25 | α = 90 |
b = 94.842 | β = 90 |
c = 121.439 | 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 | 2010-10-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 1.075 | NSLS | X29A |
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 | 2.4 | 100 | 93.9 | 0.08 | 13.9 | 24.5 | 20242 | 20242 | 43 |
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 | 2.4 | 2.44 | 50.6 | 0.565 | 6.5 | 535 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | Nterminal domain: composite model of pruned fragments from PDB entries 2pqq, 3d0s, 3h3u representing residues 21-102; C-terminal domain: pruned fragment from PDB entry 2zcw | 2.402 | 44.173 | 1.34 | 20242 | 20187 | 1031 | 93.67 | 0.2028 | 0.2 | 0.2555 | 5% randomly selected | 64.9012 |
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] | |
28.9091 | -15.1925 | -13.7167 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 18.071 |
f_angle_d | 1.165 |
f_chiral_restr | 0.073 |
f_bond_d | 0.008 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3328 |
Nucleic Acid Atoms | |
Solvent Atoms | 82 |
Heterogen Atoms | 70 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
CBASS | data collection |
DENZO | data reduction |