4GFQ
2.65 Angstrom Resolution Crystal Structure of Ribosome Recycling Factor (frr) from Bacillus anthracis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1EK8 | PDB ENTRY 1EK8 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 295 | protein: 7.4 mg/mL in 0.25 M sodium cloride, 0.01 M Tris-HCl, pH 8.3, screen: Classics II (H3), 0.24 M sodium malonate, pH 7.0, 20% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.1 | 60.31 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 95.548 | α = 90 |
b = 95.548 | β = 90 |
c = 95.548 | γ = 90 |
Symmetry | |
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Space Group | P 2 3 |
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 | MARMOSAIC 300 mm CCD | mirrors | 2012-06-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.07806 | APS | 21-ID-D |
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 | 2.65 | 30 | 99.3 | 0.061 | 18 | 4.3 | 8662 | 8662 | -3 | 87.2 |
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 | 2.65 | 2.7 | 100 | 0.553 | 2.5 | 4.4 | 430 |
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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1EK8 | 2.65 | 28.81 | 7596 | 7596 | 379 | 91.73 | 0.2051 | 0.2051 | 0.20264 | 0.25452 | RANDOM | 66.329 |
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 |
r_dihedral_angle_2_deg | 25.768 |
r_dihedral_angle_4_deg | 14.231 |
r_dihedral_angle_3_deg | 11.025 |
r_scangle_it | 5.903 |
r_scbond_it | 3.517 |
r_mcangle_it | 2.005 |
r_dihedral_angle_1_deg | 1.916 |
r_angle_refined_deg | 1.412 |
r_mcbond_it | 1.005 |
r_angle_other_deg | 0.746 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1458 |
Nucleic Acid Atoms | |
Solvent Atoms | 26 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
BALBES | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |