3SUR

Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12 in complex with NAG-thiazoline.


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, PEG2000, (NH4)2SO4, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2946.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.696α = 90
b = 102.094β = 90
c = 108.06γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-11-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21SPring-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
11.9500.1347.241603
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)
11.91.930.4254.81793

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 REPLACEMENTTHROUGHOUT3GH41.95039470210699.030.142180.140130.18061RANDOM13.088
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]
-0.490.7-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.57
r_dihedral_angle_4_deg16.727
r_dihedral_angle_3_deg13.304
r_dihedral_angle_1_deg5.883
r_sphericity_free3.952
r_scangle_it2.969
r_sphericity_bonded2.03
r_scbond_it1.984
r_angle_refined_deg1.365
r_mcangle_it1.277
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.57
r_dihedral_angle_4_deg16.727
r_dihedral_angle_3_deg13.304
r_dihedral_angle_1_deg5.883
r_sphericity_free3.952
r_scangle_it2.969
r_sphericity_bonded2.03
r_scbond_it1.984
r_angle_refined_deg1.365
r_mcangle_it1.277
r_rigid_bond_restr1.26
r_mcbond_it0.847
r_nbtor_refined0.303
r_nbd_refined0.187
r_symmetry_vdw_refined0.179
r_symmetry_hbond_refined0.173
r_xyhbond_nbd_refined0.148
r_chiral_restr0.105
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3909
Nucleic Acid Atoms
Solvent Atoms626
Heterogen Atoms19

Software

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