4RK2

Crystal structure of sugar transporter RHE_PF00321 from Rhizobium etli, target EFI-510806, an open conformation


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5294PROTEIN: 10 MM BIS-TRIS, 500 MM NACL, 10% GLYCEROL, 5 MM DTT; RESERVOIR: 0.1M SODIUM ACETATE, 0.1M TRIS:HCL, PH 8.5, 30% PEG 4000; CRYOPROTECTION: RESERVOIR, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.2645.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.995α = 90
b = 110.52β = 90
c = 137.276γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2014-07-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.85099.90.0790.07940.112.1141707-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.831002.211.9

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 DIFFRACTIONSADTHROUGHOUTNONE1.85071816230499.880.184950.183120.24254RANDOM46.292
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]
0.13-0.770.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.851
r_dihedral_angle_4_deg17.314
r_dihedral_angle_3_deg15.691
r_scbond_it14.141
r_scbond_other14.139
r_scangle_other13.637
r_long_range_B_other13.15
r_long_range_B_refined13.148
r_mcbond_it9.234
r_mcbond_other9.219
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.851
r_dihedral_angle_4_deg17.314
r_dihedral_angle_3_deg15.691
r_scbond_it14.141
r_scbond_other14.139
r_scangle_other13.637
r_long_range_B_other13.15
r_long_range_B_refined13.148
r_mcbond_it9.234
r_mcbond_other9.219
r_mcangle_other9.124
r_mcangle_it9.122
r_dihedral_angle_1_deg5.721
r_angle_refined_deg1.48
r_angle_other_deg0.824
r_chiral_restr0.089
r_bond_refined_d0.012
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 Atoms6088
Nucleic Acid Atoms
Solvent Atoms582
Heterogen Atoms6

Software

Software
Software NamePurpose
SHELXmodel building
ARP/wARPmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing