3GH4

Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12


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
2.2846.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.615α = 90
b = 101.981β = 90
c = 107.622γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1Photon FactoryBL-5A

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
11.85098.50.05824.45.348251
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)
11.81.8391.90.14873.6

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 1HP41.827.5245809243198.510.1380.136190.17216RANDOM11.183
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]
-0.120.6-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.618
r_dihedral_angle_4_deg16.154
r_dihedral_angle_3_deg12.428
r_dihedral_angle_1_deg5.656
r_sphericity_free3.353
r_scangle_it2.818
r_scbond_it1.809
r_sphericity_bonded1.657
r_angle_refined_deg1.244
r_mcangle_it1.173
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.618
r_dihedral_angle_4_deg16.154
r_dihedral_angle_3_deg12.428
r_dihedral_angle_1_deg5.656
r_sphericity_free3.353
r_scangle_it2.818
r_scbond_it1.809
r_sphericity_bonded1.657
r_angle_refined_deg1.244
r_mcangle_it1.173
r_rigid_bond_restr1.092
r_mcbond_it0.739
r_nbtor_refined0.307
r_nbd_refined0.189
r_symmetry_vdw_refined0.183
r_xyhbond_nbd_refined0.136
r_symmetry_hbond_refined0.131
r_chiral_restr0.088
r_bond_refined_d0.011
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 Atoms3928
Nucleic Acid Atoms
Solvent Atoms619
Heterogen Atoms9

Software

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