4MGE
1.85 Angstrom Resolution Crystal Structure of PTS System Cellobiose-specific Transporter Subunit IIB 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 | 1IIB | PDB ENTRY 1IIB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.3 | 295 | Protein: 7.5 mG/mL, 0.25 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: Classics II (B7), 0.056 M Sodium phosphate, 1.344 M Potasium phosphate; Cryo: 4.0 M Sodium formate., VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.77 | 30.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 59.788 | α = 90 |
b = 70.802 | β = 90 |
c = 84.464 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | Beryllium lenses | 2013-07-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
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 | 1.85 | 30 | 99.6 | 0.049 | 33.5 | 7.1 | 15627 | 15627 | -3 | 36.9 |
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 | 1.85 | 1.88 | 98.1 | 0.502 | 3.2 | 5.9 | 736 |
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 1IIB | 1.85 | 29.89 | 14797 | 14797 | 777 | 99.58 | 0.17841 | 0.17841 | 0.17608 | 0.22364 | RANDOM | 56.509 |
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] | |
-2.93 | -0.41 | 3.34 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.7 |
r_dihedral_angle_4_deg | 13.66 |
r_dihedral_angle_3_deg | 12.01 |
r_long_range_B_other | 9.159 |
r_long_range_B_refined | 9.149 |
r_scangle_other | 6.167 |
r_scbond_it | 4.242 |
r_scbond_other | 4.223 |
r_mcangle_it | 3.906 |
r_mcangle_other | 3.904 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1616 |
Nucleic Acid Atoms | |
Solvent Atoms | 59 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |