4J28

Crystal structure of a gh29 alpha-l-fucosidase gh29 from bacteroides thetaiotaomicron in complex with a 5-membered iminocyclitol inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4J27 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7291.1510.45% PEG 6K, 0.12M ammonium sulfate, 0.095M imidazole, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Crystal Properties
Matthews coefficientSolvent content
3.0659.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.728α = 90
b = 95.611β = 91.21
c = 96.988γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2011-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.7329.01398.30.04512.83.2128218128218
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.731.8294.50.4490.4491.73.217914

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 REPLACEMENTTHROUGHOUT4J271.7329.01128119640998.130.17170.17060.1935RANDOM34.2843
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]
4.24-0.86-0.23-3.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.448
r_dihedral_angle_4_deg18.55
r_dihedral_angle_3_deg12.653
r_dihedral_angle_1_deg5.784
r_mcangle_it3.156
r_mcbond_it2.434
r_mcbond_other2.433
r_angle_refined_deg1.533
r_angle_other_deg1.047
r_chiral_restr0.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.448
r_dihedral_angle_4_deg18.55
r_dihedral_angle_3_deg12.653
r_dihedral_angle_1_deg5.784
r_mcangle_it3.156
r_mcbond_it2.434
r_mcbond_other2.433
r_angle_refined_deg1.533
r_angle_other_deg1.047
r_chiral_restr0.103
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_bond_other_d0.005
r_gen_planes_other0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7027
Nucleic Acid Atoms
Solvent Atoms729
Heterogen Atoms96

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
REFMACphasing