4R2F

Crystal structure of sugar transporter ACHL_0255 from Arthrobacter chlorophenolicus A6, target EFI-510633, with bound laminaribiose


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7294PROTEIN: 10 MM BIS-TRIS, 500 MM NACL, 5% GLYCEROL, 5 MM DTT. RESERVOIR: 1.0 M AMMONIUM CITRATE TRIBASIC, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.9358.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.101α = 90
b = 139.101β = 90
c = 96.458γ = 120
Symmetry
Space GroupP 63 2 2

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
125099.60.1150.11533.9521.436317-5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0399.20.970.972.920.1

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 DIFFRACTIONSADTHROUGHOUT25036317108499.360.166360.165120.20695RANDOM39.489
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]
0.860.430.86-2.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.037
r_scbond_it17.886
r_scbond_other17.882
r_dihedral_angle_3_deg15.168
r_scangle_other14.367
r_long_range_B_other14.173
r_long_range_B_refined14.056
r_dihedral_angle_4_deg12.154
r_mcangle_other7.965
r_mcangle_it7.959
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.037
r_scbond_it17.886
r_scbond_other17.882
r_dihedral_angle_3_deg15.168
r_scangle_other14.367
r_long_range_B_other14.173
r_long_range_B_refined14.056
r_dihedral_angle_4_deg12.154
r_mcangle_other7.965
r_mcangle_it7.959
r_mcbond_it7.903
r_mcbond_other7.653
r_dihedral_angle_1_deg5.456
r_angle_refined_deg1.364
r_angle_other_deg0.781
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 Atoms2992
Nucleic Acid Atoms
Solvent Atoms271
Heterogen Atoms23

Software

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