3WDO
Structure of E. coli YajR transporter
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 5 | 289 | 30% PEG300, 0.1M sodium acetate, pH 5.0, VAPOR DIFFUSION, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.06 | 69.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 128.725 | α = 90 |
b = 128.725 | β = 90 |
c = 165.149 | γ = 120 |
Symmetry | |
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Space Group | P 61 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 225 mm CCD | 2012-04-13 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2012-10-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 1.0063,1.0089,0.9791 | SPring-8 | BL41XU |
2 | SYNCHROTRON | SSRF BEAMLINE BL17U | 0.9200 | SSRF | BL17U |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | |||||||||
1,2 | 3.15 | 50 | 99.6 | 14541 | 14541 | 2 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1,2 | 3.15 | 50 | 99.5 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | 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 | MAD | 3.15 | 39.168 | 1.34 | 14541 | 14472 | 707 | 99.38 | 0.2723 | 0.2714 | 0.29 | RANDOM | 65.7669 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 19.684 |
f_angle_d | 1.8 |
f_chiral_restr | 0.112 |
f_bond_d | 0.011 |
f_plane_restr | 0.011 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3419 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
SOLVE | phasing |