6LBV

Crystal structure of barley exohydrolaseI W434F mutant in complex with methyl 6-thio-beta-gentiobioside


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WLI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72771.7 M ammonium sulfate, 75 mM HEPES-NaOH buffer, pH 7, containing 7.5 mM sodium acetate and 1.2% (w/v) PEG 400
Crystal Properties
Matthews coefficientSolvent content
3.4764.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.609α = 90
b = 100.609β = 90
c = 180.38γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rCOLLIMATING MIRROR2012-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.9537Australian SynchrotronMX1

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
11.8987.8799.70.1236.824.270770
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)
11.891.940.12

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 REPLACEMENTTHROUGHOUT3WLI1.8945.9670770375799.740.13090.12940.1584RANDOM28.195
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]
0.630.63-1.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.238
r_dihedral_angle_4_deg19.124
r_dihedral_angle_3_deg13.632
r_dihedral_angle_1_deg7.253
r_angle_refined_deg2.122
r_angle_other_deg1.817
r_chiral_restr0.138
r_bond_refined_d0.023
r_gen_planes_refined0.012
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.238
r_dihedral_angle_4_deg19.124
r_dihedral_angle_3_deg13.632
r_dihedral_angle_1_deg7.253
r_angle_refined_deg2.122
r_angle_other_deg1.817
r_chiral_restr0.138
r_bond_refined_d0.023
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4568
Nucleic Acid Atoms
Solvent Atoms601
Heterogen Atoms98

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing