2VPO
High resolution structure of the periplasmic binding protein TeaA from TeaABC TRAP transporter of Halomonas elongata in complex with hydroxyectoine
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 100 MM HEPES PH 7.5, 40 MM MGCL2, 35 % PEG 3350 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.2 | 43 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 48.6 | α = 80.8 |
b = 52.1 | β = 85.7 |
c = 63.7 | γ = 78 |
Symmetry | |
---|---|
Space Group | P 1 |
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 | MARRESEARCH | 2008-12-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.8 | 20 | 96.2 | 0.01 | 8.8 | 3.8 | 53752 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.8 | 1.84 | 94 | 0.08 | 2.3 | 3.5 |
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 | OTHER | THROUGHOUT | NONE | 1.8 | 19.82 | 51005 | 2722 | 96.3 | 0.182 | 0.179 | 0.225 | RANDOM | 13.46 |
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] | |
-0.01 | 0.09 | -0.03 | -0.04 | 0.02 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.044 |
r_dihedral_angle_4_deg | 14.68 |
r_dihedral_angle_3_deg | 13.878 |
r_dihedral_angle_1_deg | 6.186 |
r_scangle_it | 4.442 |
r_scbond_it | 3.117 |
r_mcangle_it | 2.631 |
r_angle_other_deg | 1.854 |
r_mcbond_it | 1.667 |
r_angle_refined_deg | 1.411 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4935 |
Nucleic Acid Atoms | |
Solvent Atoms | 303 |
Heterogen Atoms | 24 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
ARP/wARP | phasing |