3WLN

Crystal structure of barley beta-D-glucan glucohydrolase isoenzyme EXO1 in complex with octyl-S-glucoside


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IEQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP727775mM HEPES-NaOH pH7.0 buffer, 1.2% PEG 400, 1.7M ammonium sulphate , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.5465.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.703α = 90
b = 100.703β = 90
c = 181.878γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315collimating mirror, double-crystal Si(111) monochromator2008-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1288.0599.960745607451
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)
11.9982.0598.70.991.3

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 REPLACEMENTTHROUGHOUT1IEQ241.4460745324599.880.171230.169420.20485RANDOM32.212
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]
0.210.21-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.447
r_dihedral_angle_4_deg15.748
r_dihedral_angle_3_deg13.903
r_dihedral_angle_1_deg6.233
r_scangle_it2.525
r_scbond_it1.578
r_angle_refined_deg1.372
r_mcangle_it0.839
r_mcbond_it0.504
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.447
r_dihedral_angle_4_deg15.748
r_dihedral_angle_3_deg13.903
r_dihedral_angle_1_deg6.233
r_scangle_it2.525
r_scbond_it1.578
r_angle_refined_deg1.372
r_mcangle_it0.839
r_mcbond_it0.504
r_nbtor_refined0.303
r_symmetry_vdw_refined0.251
r_symmetry_hbond_refined0.228
r_nbd_refined0.195
r_xyhbond_nbd_refined0.169
r_chiral_restr0.09
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms4566
Nucleic Acid Atoms
Solvent Atoms901
Heterogen Atoms172

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling