2P2F
Acetyl-CoA Synthetase, wild-type with acetate, AMP, and CoA bound
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1PG4 | pdb entry 1PG4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 287 | 6-15% PEG 8000, 9-13% ethylene glycol, 50 mM BTP, 1 mM CoA, 1 mM Acetate, 1 mM AMP, 1 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.42 | 49.07 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 90.906 | α = 90 |
b = 94.933 | β = 90 |
c = 161.814 | 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 | 113 | CCD | CUSTOM-MADE | 2003-03-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X12C | 0.95 | NSLS | X12C |
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 | 2.58 | 81.65 | 98.9 | 0.072 | 10.8 | 5.1 | 42079 | 38.3 |
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 | 2.58 | 2.7 | 100 | 0.224 | 1 |
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 | FOURIER SYNTHESIS | THROUGHOUT | pdb entry 1PG4 | 2.58 | 81.65 | 42079 | 2261 | 98.97 | 0.186 | 0.183 | 0.247 | RANDOM | 18.048 |
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] | |
0.71 | -1.14 | 0.43 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.148 |
r_dihedral_angle_4_deg | 20.21 |
r_dihedral_angle_3_deg | 15.837 |
r_dihedral_angle_1_deg | 6.416 |
r_scangle_it | 2.681 |
r_scbond_it | 1.672 |
r_angle_refined_deg | 1.532 |
r_mcangle_it | 1.019 |
r_mcbond_it | 0.611 |
r_nbtor_refined | 0.31 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9828 |
Nucleic Acid Atoms | |
Solvent Atoms | 159 |
Heterogen Atoms | 150 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
REFMAC | phasing |