4RY0 | pdb_00004ry0

Crystal structure of ribose transporter solute binding protein RHE_PF00037 from Rhizobium etli CFN 42, TARGET EFI-511357, in complex with D-ribose


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM D-RIBOSE); RESERVOIR: 0.2 M CALCIUM CHLORIDE, 0.1 M TRIS-HCL, PH 8.5, 20% (w/v) PEG 4000; CRYOPROTECTION: RESERVOIR SOLUTION PLUS 20% D-GLUCOSE SOLUTION; VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties
Matthews coefficientSolvent content
2.3647.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.11α = 90
b = 36.766β = 117.91
c = 95.48γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEMIRRORS2014-12-05MSINGLE 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
11.450980.10322.27.557304-3
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)
11.41.4296.60.82.577.5

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.42453653172497.660.14460.143410.160.181060.2RANDOM19.268
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]
-0.65-1.083.84-1.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.674
r_sphericity_free30.549
r_sphericity_bonded15.754
r_dihedral_angle_3_deg14.736
r_dihedral_angle_4_deg10.484
r_scbond_it7.959
r_scbond_other7.959
r_scangle_other6.98
r_long_range_B_refined6.434
r_long_range_B_other6.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.674
r_sphericity_free30.549
r_sphericity_bonded15.754
r_dihedral_angle_3_deg14.736
r_dihedral_angle_4_deg10.484
r_scbond_it7.959
r_scbond_other7.959
r_scangle_other6.98
r_long_range_B_refined6.434
r_long_range_B_other6.34
r_dihedral_angle_1_deg5.661
r_rigid_bond_restr4.404
r_mcangle_other3.337
r_mcangle_it3.314
r_mcbond_other3.232
r_mcbond_it3.196
r_angle_refined_deg1.537
r_angle_other_deg1.448
r_chiral_restr0.09
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2120
Nucleic Acid Atoms
Solvent Atoms261
Heterogen Atoms12

Software

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