3WLJ

Crystal structure of barley beta-D-glucan glucohydrolase isoenzyme EXO1 in complex with 3-deoxy-glucose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X39PDB ENTRY 1X39

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP727775mM HEPES-NaOH pH7.0 buffer, 1.2% PEG 400, 1.7M ammonium sulphate , pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.5565.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.816α = 90
b = 100.816β = 90
c = 181.646γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHRH COATED SI MIRROR2005-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-ID-B1.12714APS14-ID-B

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
11.6734.18990.05257.813.3101919
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)
11.671.7294.70.6191.117.1

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 1X391.6734.18101919536298.960.160090.158790.18478RANDOM26.369
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]
0.30.3-0.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.021
r_dihedral_angle_3_deg13.357
r_dihedral_angle_4_deg13.005
r_dihedral_angle_1_deg5.983
r_rigid_bond_restr5.169
r_scbond_it4.696
r_sphericity_free4.546
r_sphericity_bonded4.463
r_scangle_it4.193
r_mcangle_it1.518
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.021
r_dihedral_angle_3_deg13.357
r_dihedral_angle_4_deg13.005
r_dihedral_angle_1_deg5.983
r_rigid_bond_restr5.169
r_scbond_it4.696
r_sphericity_free4.546
r_sphericity_bonded4.463
r_scangle_it4.193
r_mcangle_it1.518
r_angle_refined_deg1.408
r_mcbond_it1.024
r_nbtor_refined0.308
r_symmetry_vdw_refined0.234
r_symmetry_hbond_refined0.217
r_nbd_refined0.2
r_xyhbond_nbd_refined0.146
r_chiral_restr0.098
r_bond_refined_d0.013
r_gen_planes_refined0.005
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4566
Nucleic Acid Atoms
Solvent Atoms830
Heterogen Atoms217

Software

Software
Software NamePurpose
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing