1PE1
Aquifex aeolicus KDO8PS in complex with cadmium and 2-PGA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1FWS | PDB ENTRY 1FWS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.8 | 281 | PEG4000, Na-acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.76 | 55.43 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 84.434 | α = 90 |
b = 84.434 | β = 90 |
c = 159.751 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 | IMAGE PLATE | RIGAKU RAXIS IV | Osmic mirrors | 2002-12-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU300 | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.74 | 43.05 | 88.8 | 0.064 | 0.064 | 6.5 | 16.6 | 60903 | 60747 | 1 | 35.9 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.74 | 1.8 | 25.9 | 0.283 | 0.283 | 2.4 | 3.3 | 1751 |
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 (All) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | PDB ENTRY 1FWS | 1.74 | 43.05 | 60903 | 60747 | 5937 | 88.8 | 0.193 | 0.193 | 0.237 | RANDOM | 35.2 |
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] | |
4.66 | 3.12 | 4.66 | -9.32 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.6 |
c_scangle_it | 7.48 |
c_scbond_it | 6.19 |
c_mcangle_it | 5.25 |
c_mcbond_it | 4.53 |
c_angle_deg | 2 |
c_improper_angle_d | 1.37 |
c_bond_d | 0.023 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4056 |
Nucleic Acid Atoms | |
Solvent Atoms | 471 |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
CrystalClear | data reduction |
d*TREK | data scaling |
CNS | phasing |