2Y2W

Elucidation of the substrate specificity and protein structure of AbfB, a family 51 alpha-L-arabinofuranosidase from Bifidobacterium longum.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PZ3PDB ENTRY 1PZ3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSIONABFB CRYSTALS WERE OBTAINED BY MIXING 1 MICROLITER CONCENTRATED PROTEIN SOLUTION WITH 3 MICROLITER CRYSTALLIZATION SOLUTION CONTAINING 0.2 M SODIUM PHOSPHATE MONOBASIC MONOHYDRATE, 20% W/V POLYETHYLENE GLYCOL 3350, USING THE VAPOR-DIFFUSION METHOD WITH HANGING OR SITTING DROPS AT 20-24 C.
Crystal Properties
Matthews coefficientSolvent content
2.4437

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.469α = 90
b = 165.811β = 90
c = 184.297γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
12.52099.80.128.94.11091832.4
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)
12.52.641000.562.44.1

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1PZ32.520109183577699.820.222630.220140.26986RANDOM37.259
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]
-0.71-2.593.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.517
r_dihedral_angle_3_deg15.029
r_dihedral_angle_4_deg14.891
r_dihedral_angle_1_deg4.965
r_angle_refined_deg0.92
r_scangle_it0.694
r_mcangle_it0.439
r_scbond_it0.396
r_mcbond_it0.236
r_chiral_restr0.062
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.517
r_dihedral_angle_3_deg15.029
r_dihedral_angle_4_deg14.891
r_dihedral_angle_1_deg4.965
r_angle_refined_deg0.92
r_scangle_it0.694
r_mcangle_it0.439
r_scbond_it0.396
r_mcbond_it0.236
r_chiral_restr0.062
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms23544
Nucleic Acid Atoms
Solvent Atoms699
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing