6LC5

Crystal structure of barley exohydrolaseI W434F in complex with 4'-nitrophenyl thiolaminaribioside


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
3.4764.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.774α = 90
b = 100.774β = 90
c = 180.169γ = 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
11.7687.9599.90.11936.513.787843
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)
11.761.80.119

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 REPLACEMENTTHROUGHOUT3WLI1.7645.9687843463199.870.14120.13970.1689RANDOM25.221
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]
0.150.15-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.181
r_dihedral_angle_4_deg16.059
r_dihedral_angle_3_deg13.33
r_dihedral_angle_1_deg8.319
r_angle_refined_deg2.617
r_angle_other_deg1.856
r_chiral_restr0.166
r_bond_refined_d0.027
r_gen_planes_refined0.012
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.181
r_dihedral_angle_4_deg16.059
r_dihedral_angle_3_deg13.33
r_dihedral_angle_1_deg8.319
r_angle_refined_deg2.617
r_angle_other_deg1.856
r_chiral_restr0.166
r_bond_refined_d0.027
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4568
Nucleic Acid Atoms
Solvent Atoms502
Heterogen Atoms206

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing