4RYA

Crystal structure of abc transporter solute binding protein AVI_3567 from AGROBACTERIUM VITIS S4, TARGET EFI-510645, with bound D-mannitol


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM D-MANNITOL), RESERVOIR: 0.085 M TRIS-HCL, PH 8.5, 0.17 M SODIUM ACETATE, 25% PEG3350, 15% (V/V) GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties
Matthews coefficientSolvent content
2.4850.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.413α = 90
b = 61.256β = 104.01
c = 65.501γ = 90
Symmetry
Space GroupP 1 21 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
11.55099.30.12212.957.573250-3
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)
11.51.5398.40.494.57.4

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 DIFFRACTIONSADTHROUGHOUT1.52569767217898.370.133140.132040.16824RANDOM24.318
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]
0.77-0.99-0.790.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.747
r_sphericity_free23.465
r_dihedral_angle_4_deg19.609
r_sphericity_bonded14.332
r_dihedral_angle_3_deg13.48
r_scbond_it7.253
r_scbond_other7.252
r_scangle_other6.365
r_dihedral_angle_1_deg5.834
r_long_range_B_refined5.705
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.747
r_sphericity_free23.465
r_dihedral_angle_4_deg19.609
r_sphericity_bonded14.332
r_dihedral_angle_3_deg13.48
r_scbond_it7.253
r_scbond_other7.252
r_scangle_other6.365
r_dihedral_angle_1_deg5.834
r_long_range_B_refined5.705
r_long_range_B_other5.705
r_mcangle_other3.855
r_mcangle_it3.854
r_mcbond_it3.367
r_mcbond_other3.365
r_rigid_bond_restr3.294
r_angle_refined_deg1.565
r_angle_other_deg0.91
r_chiral_restr0.095
r_bond_refined_d0.012
r_gen_planes_refined0.009
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3234
Nucleic Acid Atoms
Solvent Atoms466
Heterogen Atoms16

Software

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