3AHF
Phosphoketolase from Bifidobacterium Breve complexed with inorganic phosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3AHC | PDB ENTRY 3AHC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 9 | 293 | 24%(v/v) PEG 6000, 0.1M BICINE buffer, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.33 | 63.07 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 173.906 | α = 90 |
b = 173.906 | β = 90 |
c = 163.522 | γ = 90 |
Symmetry | |
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Space Group | I 4 2 2 |
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 4r | mirrors | 2008-10-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-6A | 1.0000 | Photon Factory | BL-6A |
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 | 2.3 | 50 | 100 | 0.108 | 24.9 | 11.4 | 55669 | 55630 | 28.3 |
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) | |||||||||||
2.3 | 2.38 | 100 | 0.355 | 4.7 | 10.4 | 5490 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 3AHC | 2.3 | 40.88 | 55630 | 52685 | 2814 | 99.72 | 0.17929 | 0.17676 | 0.22608 | RANDOM | 28.516 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.541 |
r_dihedral_angle_4_deg | 20.762 |
r_dihedral_angle_3_deg | 15.852 |
r_dihedral_angle_1_deg | 7.141 |
r_scangle_it | 4.53 |
r_scbond_it | 3.028 |
r_angle_refined_deg | 1.904 |
r_mcangle_it | 1.671 |
r_mcbond_it | 0.964 |
r_chiral_restr | 0.141 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6379 |
Nucleic Acid Atoms | |
Solvent Atoms | 518 |
Heterogen Atoms | 50 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
REFMAC | phasing |