4WBS
Crystal structure of an ABC transporter related protein from Burkholderia phymatum
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1Z47 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | JCSG-2, condition B5, optimized: 1M LiCl, 100mM Tris pH 8.5, 20% PEG 6000; cryo: 20% EDO; BuphA.00057.b.A1.PS01348 at 20mg/ml with 1mM ATP (invisible in electron density; tray 233360f3, puck wlt6-3 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.07 | α = 90 |
b = 79.85 | β = 90 |
c = 121.14 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | ADSC QUANTUM 315r | 2012-10-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 0.97740 | ALS | 5.0.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 50 | 99.7 | 0.065 | 0.073 | 16.05 | 5 | 36187 | 36187 | -3 | 29.54 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2 | 2.05 | 100 | 0.586 | 0.652 | 3.15 | 5.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1Z47 | 2 | 44.771 | 1.35 | 36131 | 2029 | 99.77 | 0.1862 | 0.1831 | 0.2373 | 37.505 |
Temperature Factor Modeling | ||||||
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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 |
f_dihedral_angle_d | 12.547 |
f_angle_d | 1.116 |
f_chiral_restr | 0.044 |
f_bond_d | 0.008 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3708 |
Nucleic Acid Atoms | |
Solvent Atoms | 288 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
BALBES | phasing |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
XSCALE | data scaling |