3GH7

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HP4PDB 1HP4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6293Na-Acetate, PEG2000, 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 = 95.667α = 90
b = 102.123β = 90
c = 108.074γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 3152007-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0000SPring-8BL41XU

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
11.95097.90.11712.24.441113
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)
11.91.9391.50.2543.42.9

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 REPLACEMENTTHROUGHOUTPDB 1HP41.934.9139027207197.880.141810.139780.18004RANDOM9.92
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]
-0.090.37-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.196
r_dihedral_angle_4_deg15.441
r_dihedral_angle_3_deg12.72
r_dihedral_angle_1_deg5.756
r_sphericity_free4.056
r_scangle_it2.944
r_scbond_it1.919
r_sphericity_bonded1.785
r_angle_refined_deg1.313
r_mcangle_it1.229
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.196
r_dihedral_angle_4_deg15.441
r_dihedral_angle_3_deg12.72
r_dihedral_angle_1_deg5.756
r_sphericity_free4.056
r_scangle_it2.944
r_scbond_it1.919
r_sphericity_bonded1.785
r_angle_refined_deg1.313
r_mcangle_it1.229
r_rigid_bond_restr1.191
r_mcbond_it0.797
r_nbtor_refined0.309
r_nbd_refined0.188
r_symmetry_vdw_refined0.188
r_symmetry_hbond_refined0.171
r_xyhbond_nbd_refined0.144
r_chiral_restr0.09
r_bond_refined_d0.012
r_gen_planes_refined0.005
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 Atoms3922
Nucleic Acid Atoms
Solvent Atoms562
Heterogen Atoms20

Software

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