1DAK
DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX REACTION INTERMEDIATE ADP AND MIXED ANHYDRIDE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1DAH | PDB ENTRY 1DAH, WITH NON-PROTEIN ATOMS EXCLUDED |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 8.5 | pH 8.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.13 | 42.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 72.68 | α = 90 |
b = 48.19 | β = 106.58 |
c = 61.07 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | PRINCETON 2K | 1997-10-31 | M |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID09 | ESRF | ID09 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.6 | 25 | 99 | 0.078 | 16 | 3.2 | 86120 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.6 | 1.66 | 92.4 | 0.43 | 2.8 | 2.6 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | DIFFERENCE FOURIER | THROUGHOUT | PDB ENTRY 1DAH, WITH NON-PROTEIN ATOMS EXCLUDED | 1.6 | 20 | 29418 | 1505 | 99 | 0.184 | 0.21 | RANDOM | 13.6 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
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 |
p_staggered_tor | 15.9 |
p_planar_tor | 3.1 |
p_scangle_it | 1.949 |
p_mcangle_it | 1.335 |
p_scbond_it | 1.227 |
p_mcbond_it | 0.862 |
p_multtor_nbd | 0.258 |
p_singtor_nbd | 0.172 |
p_chiral_restr | 0.081 |
p_planar_d | 0.021 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1692 |
Nucleic Acid Atoms | |
Solvent Atoms | 216 |
Heterogen Atoms | 54 |
Software
Software | |
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Software Name | Purpose |
CCP4 | model building |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
CCP4 | phasing |