4RY8

Crystal structure of 5-methylthioribose transporter solute binding protein TLET_1677 from Thermotoga lettingae TMO TARGET EFI-511109 in complex with 5-methylthioribose


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5294PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT); RESERVOIR: 0.1 M HEPES-NAOH, PH 7.5, 0.2 M MAGNESIUM CHLORIDE, 30% PPG P400; CRYOPROTECTION: RESERVOIR SOLUTION; VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K;
Crystal Properties
Matthews coefficientSolvent content
2.2344.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.622α = 91.83
b = 67.848β = 92.39
c = 83.653γ = 89.93
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEMIRRORS2014-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-IDAPS31-ID

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
11.755097.10.137103.9128230-3
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)
11.751.7894.90.712.13.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.7550119981377196.950.215930.214440.26356RANDOM33.26
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]
-3.67-0.31-0.41-3.80.377.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.484
r_dihedral_angle_4_deg20.369
r_dihedral_angle_3_deg14.933
r_long_range_B_refined11.642
r_long_range_B_other11.642
r_scangle_other11.181
r_scbond_it10.856
r_scbond_other10.855
r_dihedral_angle_1_deg6.368
r_mcangle_other6.184
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.484
r_dihedral_angle_4_deg20.369
r_dihedral_angle_3_deg14.933
r_long_range_B_refined11.642
r_long_range_B_other11.642
r_scangle_other11.181
r_scbond_it10.856
r_scbond_other10.855
r_dihedral_angle_1_deg6.368
r_mcangle_other6.184
r_mcangle_it6.182
r_mcbond_it5.672
r_mcbond_other5.665
r_angle_refined_deg1.601
r_angle_other_deg0.835
r_chiral_restr0.091
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9868
Nucleic Acid Atoms
Solvent Atoms476
Heterogen Atoms44

Software

Software
Software NamePurpose
SHELXmodel building
ARP/wARPmodel building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing