3WLM

Crystal structure of barley beta-D-glucan glucohydrolase isoenzyme exo1 in complex with octyl-O-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
3.5565.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.019α = 90
b = 101.019β = 90
c = 180.798γ = 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) monochromator2005-11-12MSINGLE 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
11.942.2610070533705331
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)
11.91.9599.50.991.05

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 REPLACEMENTTHROUGHOUT1IEQ1.942.2670533374099.960.171150.169560.20133RANDOM25.572
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]
-0.05-0.050.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.326
r_dihedral_angle_4_deg14.571
r_dihedral_angle_3_deg13.652
r_dihedral_angle_1_deg6.008
r_scangle_it2.527
r_scbond_it1.592
r_angle_refined_deg1.266
r_mcangle_it0.803
r_mcbond_it0.496
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.326
r_dihedral_angle_4_deg14.571
r_dihedral_angle_3_deg13.652
r_dihedral_angle_1_deg6.008
r_scangle_it2.527
r_scbond_it1.592
r_angle_refined_deg1.266
r_mcangle_it0.803
r_mcbond_it0.496
r_nbtor_refined0.303
r_symmetry_hbond_refined0.239
r_symmetry_vdw_refined0.229
r_nbd_refined0.194
r_xyhbond_nbd_refined0.165
r_chiral_restr0.085
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4566
Nucleic Acid Atoms
Solvent Atoms870
Heterogen Atoms122

Software

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