3LT8
A non-biological ATP binding protein with a single point mutation (D65V), that contributes to optimized folding and ligand binding, crystallized in the presence of 100 mM ATP.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3G4B | PDB ENTRY 3G4B |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8.5 | 0.1 M SODIUM PHOSPHATE PH 8.5, 0.25 M SODIUM CITRATE, 0.3 M SODIUM CHLORIDE, 23% PEG 400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.22 | 70.86 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 71.461 | α = 90 |
b = 71.461 | β = 90 |
c = 55.583 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 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 4 | 2008-06-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X12B | NSLS | X12B |
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 | 2.55 | 50 | 99.9 | 0.092 | 25.481 | 5.6 | 5562 |
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) | |||||||||||
2.55 | 2.64 | 100 | 0.494 | 5.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | PDB ENTRY 3G4B | 2.55 | 41.34 | 5558 | 251 | 100 | 0.181 | 0.178 | 0.239 | RANDOM | 33.46 |
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] | |
-0.01 | -0.01 | -0.01 | 0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.661 |
r_dihedral_angle_3_deg | 18.144 |
r_dihedral_angle_4_deg | 17.925 |
r_dihedral_angle_1_deg | 5.412 |
r_scangle_it | 4.356 |
r_scbond_it | 2.498 |
r_angle_refined_deg | 1.71 |
r_mcangle_it | 1.547 |
r_mcbond_it | 0.773 |
r_chiral_restr | 0.112 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 583 |
Nucleic Acid Atoms | |
Solvent Atoms | 31 |
Heterogen Atoms | 50 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |