3SUV

Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12 in complex with NHAc-DNJ


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6293Na-acetate, PEG 2000, (NH4)2SO4, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2946.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.553α = 90
b = 101.993β = 90
c = 108.09γ = 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
11.6500.0867.569747
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)
11.61.660.3187.4

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 REPLACEMENTTHROUGHOUT3GH41.65066194352199.990.145130.143710.17134RANDOM11.484
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]
-0.460.57-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.281
r_dihedral_angle_4_deg16.14
r_dihedral_angle_3_deg11.919
r_dihedral_angle_1_deg5.627
r_sphericity_free2.667
r_scangle_it2.477
r_scbond_it1.661
r_sphericity_bonded1.625
r_angle_refined_deg1.198
r_mcangle_it1.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.281
r_dihedral_angle_4_deg16.14
r_dihedral_angle_3_deg11.919
r_dihedral_angle_1_deg5.627
r_sphericity_free2.667
r_scangle_it2.477
r_scbond_it1.661
r_sphericity_bonded1.625
r_angle_refined_deg1.198
r_mcangle_it1.06
r_rigid_bond_restr0.915
r_mcbond_it0.675
r_nbtor_refined0.31
r_nbd_refined0.191
r_symmetry_vdw_refined0.174
r_symmetry_hbond_refined0.155
r_xyhbond_nbd_refined0.117
r_chiral_restr0.082
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 Atoms760
Heterogen Atoms19

Software

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