3OGH
Crystal structure of yciE protein from E. coli CFT073, a member of ferritine-like superfamily of diiron-containing four-helix-bundle proteins
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 291 | 25% Peg 3350, 0.2 M Magnesium Chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.96 | 37.27 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 30.148 | α = 90 |
b = 90.295 | β = 103.51 |
c = 58.132 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 315r | mirrors | 2010-02-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.9794 | APS | 19-ID |
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 | 1.65 | 40 | 99.8 | 0.083 | 29 | 3.7 | 36700 | 36634 | 2 | 2 |
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) | |||||||||||
1.65 | 1.68 | 99.5 | 0.367 | 4 | 3.5 | 1843 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.65 | 40 | 36311 | 34496 | 1815 | 99.46 | 0.18 | 0.16878 | 0.16648 | 0.21291 | RANDOM | 25.968 |
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] | |
-0.14 | -0.91 | -1.96 | 1.68 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.453 |
r_dihedral_angle_3_deg | 13.441 |
r_dihedral_angle_4_deg | 10.732 |
r_scangle_it | 6.65 |
r_mcbond_other | 5.601 |
r_dihedral_angle_1_deg | 4.869 |
r_scbond_it | 4.221 |
r_mcangle_it | 3.304 |
r_rigid_bond_restr | 2.408 |
r_mcbond_it | 1.88 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2353 |
Nucleic Acid Atoms | |
Solvent Atoms | 196 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
SBC-Collect | data collection |
HKL-3000 | phasing |
SHELX | model building |
ARP/wARP | model building |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
SHELX | phasing |