2W5O | pdb_00002w5o

Complex structure of the GH93 alpha-L-arabinofuranosidase of Fusarium graminearum with arabinobiose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.522% PEG 4K, 100 MM HEPES 7.5, 50 MM AMSO4, 20% GLYCEROL FOR CRYOPROTECTION
Crystal Properties
Matthews coefficientSolvent content
2.7855.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.62α = 90
b = 86.88β = 90
c = 108.17γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
12.0548.6299.90.138.33.7295322
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)
12.052.1699.80.432.83.8

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUTPDB ENTRY 2W5N2.0545.9327981149899.90.1710.1680.170.2160.22RANDOM14.59
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]
-0.38-0.160.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.661
r_dihedral_angle_4_deg17.419
r_dihedral_angle_3_deg12.895
r_dihedral_angle_1_deg6.993
r_scangle_it3.066
r_scbond_it2.029
r_angle_refined_deg1.584
r_mcangle_it1.18
r_mcbond_it0.669
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.661
r_dihedral_angle_4_deg17.419
r_dihedral_angle_3_deg12.895
r_dihedral_angle_1_deg6.993
r_scangle_it3.066
r_scbond_it2.029
r_angle_refined_deg1.584
r_mcangle_it1.18
r_mcbond_it0.669
r_chiral_restr0.101
r_bond_refined_d0.015
r_gen_planes_refined0.008
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 Atoms2848
Nucleic Acid Atoms
Solvent Atoms318
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing