3SUU

Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12 in complex with Gal-PUGNAc


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GH4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6293Na-citrate, PEG 2000, (NH4)2SO4, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.346.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.439α = 90
b = 102.626β = 90
c = 108.236γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21.0000SPring-8BL26B2

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
11.6500.0977.570177
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.660.3747.4

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 REPLACEMENTTHROUGHOUT3GH41.65066605353899.990.145230.143940.16915RANDOM10.779
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]
-0.14-0.020.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.413
r_dihedral_angle_4_deg15.561
r_dihedral_angle_3_deg11.944
r_dihedral_angle_1_deg5.598
r_sphericity_free2.716
r_scangle_it2.551
r_scbond_it1.683
r_sphericity_bonded1.545
r_angle_refined_deg1.231
r_mcangle_it1.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.413
r_dihedral_angle_4_deg15.561
r_dihedral_angle_3_deg11.944
r_dihedral_angle_1_deg5.598
r_sphericity_free2.716
r_scangle_it2.551
r_scbond_it1.683
r_sphericity_bonded1.545
r_angle_refined_deg1.231
r_mcangle_it1.071
r_rigid_bond_restr0.935
r_mcbond_it0.685
r_nbtor_refined0.311
r_nbd_refined0.191
r_symmetry_vdw_refined0.17
r_xyhbond_nbd_refined0.119
r_symmetry_hbond_refined0.111
r_chiral_restr0.086
r_bond_refined_d0.008
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3909
Nucleic Acid Atoms
Solvent Atoms772
Heterogen Atoms30

Software

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