2YDT

STRUCTURE OF THE ALPHA-L-ARABINOFURANOSIDASE ARB93A from FUSARIUM Graminearum in complexe with an iminosugar inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2W5NPDB ENTRY 2W5N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.538% PEG 550MME, 100 MM HEPES PH 7.5, 100 MM MNSO4.
Crystal Properties
Matthews coefficientSolvent content
2.3748.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.435α = 90
b = 105.435β = 90
c = 140.038γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2010-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30AESRFBM30A

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
11.644.691000.06117.6551072
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)
11.61.6799.80.3825

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 2W5N1.644.6949382265699.90.1440.1420.17RANDOM9.74
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]
0.160.16-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.881
r_dihedral_angle_4_deg13.312
r_dihedral_angle_3_deg12.405
r_dihedral_angle_1_deg7.279
r_scangle_it3.356
r_scbond_it2.141
r_angle_refined_deg1.604
r_mcangle_it1.407
r_angle_other_deg0.937
r_mcbond_it0.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.881
r_dihedral_angle_4_deg13.312
r_dihedral_angle_3_deg12.405
r_dihedral_angle_1_deg7.279
r_scangle_it3.356
r_scbond_it2.141
r_angle_refined_deg1.604
r_mcangle_it1.407
r_angle_other_deg0.937
r_mcbond_it0.84
r_mcbond_other0.258
r_chiral_restr0.101
r_bond_refined_d0.016
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_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 Atoms2848
Nucleic Acid Atoms
Solvent Atoms524
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing