5M34
Structure of cobinamide-bound BtuF mutant W66Y, 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 | ||||
---|---|---|---|---|
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 |
2.4 | 48.73 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 139.83 | α = 90 |
b = 90.8 | β = 111.25 |
c = 51.07 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.6 | 29.48 | 93.24 | 9.77 | 2.8 | 73585 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.6 | 29.48 | 69926 | 3640 | 93.24 | 0.19327 | 0.19113 | 0.23334 | RANDOM | 33.197 |
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] | |
38.04 | 10.48 | -22.89 | -15.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.698 |
r_dihedral_angle_4_deg | 20.179 |
r_dihedral_angle_3_deg | 15.384 |
r_long_range_B_refined | 7.879 |
r_long_range_B_other | 7.879 |
r_dihedral_angle_1_deg | 7.651 |
r_scangle_other | 5.084 |
r_mcangle_it | 4.194 |
r_mcangle_other | 4.194 |
r_scbond_it | 3.514 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3539 |
Nucleic Acid Atoms | |
Solvent Atoms | 499 |
Heterogen Atoms | 154 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
XSCALE | data scaling |
PHENIX | phasing |