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
IDMethodpHTemperatureDetails
1100 MM HEPES PH 7.5, 40 MM MGCL2, 35 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.243

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.6α = 80.8
b = 52.1β = 85.7
c = 63.7γ = 78
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2008-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.82096.20.018.83.8537522
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.84940.082.33.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONOTHERTHROUGHOUTNONE1.819.8251005272296.30.1820.1790.225RANDOM13.46
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]
-0.010.09-0.03-0.040.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.044
r_dihedral_angle_4_deg14.68
r_dihedral_angle_3_deg13.878
r_dihedral_angle_1_deg6.186
r_scangle_it4.442
r_scbond_it3.117
r_mcangle_it2.631
r_angle_other_deg1.854
r_mcbond_it1.667
r_angle_refined_deg1.411
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.044
r_dihedral_angle_4_deg14.68
r_dihedral_angle_3_deg13.878
r_dihedral_angle_1_deg6.186
r_scangle_it4.442
r_scbond_it3.117
r_mcangle_it2.631
r_angle_other_deg1.854
r_mcbond_it1.667
r_angle_refined_deg1.411
r_mcbond_other0.457
r_chiral_restr0.075
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4935
Nucleic Acid Atoms
Solvent Atoms303
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
ARP/wARPphasing