5TSE
2.35 Angstrom Crystal Structure Minor Lipoprotein from Acinetobacter baumannii.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3BF2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.3 | 295 | Protein: 15.9 mg/ml, 0.01M Tris HCl (pH 8.3), Screen: JCSG+ (A8), 0.2M Ammonium formate, 20% (w/v) PEG 3350. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.806 | α = 90 |
b = 68.806 | β = 90 |
c = 96.586 | γ = 90 |
Symmetry | |
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Space Group | P 41 |
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 | 2016-08-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
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 | 2.35 | 30 | 100 | 0.058 | 0.058 | 31.5 | 7.5 | 18791 | -3 | 63.4 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.35 | 2.39 | 99.8 | 0.723 | 0.682 | 2.1 | 5.5 |
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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3BF2 | 2.35 | 29.32 | 17811 | 953 | 99.88 | 0.2182 | 0.21569 | 0.2628 | RANDOM | 70.732 |
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] | |
1.58 | 1.58 | -3.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.456 |
r_dihedral_angle_4_deg | 10.981 |
r_dihedral_angle_3_deg | 9.085 |
r_long_range_B_refined | 7.174 |
r_long_range_B_other | 7.169 |
r_scangle_other | 4.11 |
r_mcangle_it | 3.974 |
r_mcangle_other | 3.973 |
r_scbond_it | 2.532 |
r_scbond_other | 2.531 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3210 |
Nucleic Acid Atoms | |
Solvent Atoms | 59 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
MOLREP | phasing |