3OZP

Crystal Structure of insect beta-N-acetyl-D-hexosaminidase OfHex1 complexed with PUGNAc


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O7A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7277100mM HEPES, 200mM MgCl2, 30% PEG400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
4.5172.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.09α = 90
b = 108.09β = 90
c = 175.28γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277CCDMARMOSAIC 225 mm CCD2009-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.9753SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1227.52100728887288822

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1o7a227.5272888728881000.199080.1990829.302
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]
-0.01-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.825
r_dihedral_angle_4_deg18.687
r_dihedral_angle_3_deg15.16
r_dihedral_angle_1_deg5.468
r_scangle_it1.842
r_angle_refined_deg1.077
r_scbond_it1.074
r_mcangle_it0.755
r_mcbond_it0.384
r_chiral_restr0.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.825
r_dihedral_angle_4_deg18.687
r_dihedral_angle_3_deg15.16
r_dihedral_angle_1_deg5.468
r_scangle_it1.842
r_angle_refined_deg1.077
r_scbond_it1.074
r_mcangle_it0.755
r_mcbond_it0.384
r_chiral_restr0.081
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4615
Nucleic Acid Atoms
Solvent Atoms613
Heterogen Atoms25

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling