5ULB

Crystal structure of sugar ABC transporter from Yersinia enterocolitica subsp. enterocolitica 8081


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52910.1 M Bis-Tris pH 6.5, 28% w/v PEG MME 2000
Crystal Properties
Matthews coefficientSolvent content
2.1241.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.993α = 90
b = 55.856β = 90
c = 119.573γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rdouble crystal2013-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9794APS19-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
11.284099.20.12205.778779
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)
11.281.392.60.8

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 DIFFRACTIONTHROUGHOUT1.284063186334293.80.1120.110.153RANDOM18.48
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]
-0.640.510.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.534
r_sphericity_free36.859
r_sphericity_bonded16.008
r_dihedral_angle_4_deg15.638
r_dihedral_angle_3_deg12.889
r_long_range_B_refined6.265
r_dihedral_angle_1_deg5.763
r_scangle_other5.623
r_scbond_it5.096
r_rigid_bond_restr5.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.534
r_sphericity_free36.859
r_sphericity_bonded16.008
r_dihedral_angle_4_deg15.638
r_dihedral_angle_3_deg12.889
r_long_range_B_refined6.265
r_dihedral_angle_1_deg5.763
r_scangle_other5.623
r_scbond_it5.096
r_rigid_bond_restr5.095
r_scbond_other5.094
r_long_range_B_other4.822
r_mcangle_other3.464
r_mcangle_it3.463
r_mcbond_it3.118
r_mcbond_other3.051
r_angle_refined_deg2.221
r_angle_other_deg1.191
r_chiral_restr0.152
r_bond_refined_d0.027
r_gen_planes_refined0.012
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 Atoms2531
Nucleic Acid Atoms
Solvent Atoms389
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing