5M3B
Structure of cobinamide-bound BtuF mutant W66L, the periplasmic vitamin B12 binding protein in E.coli
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5M29 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293.15 | PEG3350 HEPES pH 7 Tryptone |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 47.19 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 136.28 | α = 90 |
b = 90.46 | β = 110.74 |
c = 50.81 | 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 | 123 | PIXEL | DECTRIS PILATUS 6M-F | 2014-12-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 0.97794 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.5 | 19.67 | 96.77 | 11.04 | 3 | 89061 |
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 | 5M29 | 1.5 | 19.67 | 84607 | 4454 | 96.77 | 0.19772 | 0.1961 | 0.22875 | RANDOM | 24.9 |
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] | |
1.13 | 0.18 | -1.05 | -0.16 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.546 |
r_dihedral_angle_4_deg | 18.446 |
r_dihedral_angle_3_deg | 13.204 |
r_long_range_B_other | 7.605 |
r_long_range_B_refined | 7.604 |
r_dihedral_angle_1_deg | 6.715 |
r_scangle_other | 4.667 |
r_mcangle_it | 3.371 |
r_mcangle_other | 3.371 |
r_scbond_it | 3.077 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3539 |
Nucleic Acid Atoms | |
Solvent Atoms | 555 |
Heterogen Atoms | 160 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
XSCALE | data scaling |
PHENIX | phasing |