3NSM

Crystal Structure of insect beta-N-acetyl-D-hexosaminidase OfHex1 from Ostrinia furnacalis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O7APDB ENTRY 1o7a

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7277100mM HEPES, 200mM MgCl2, 30% PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
4.5272.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.11α = 90
b = 108.11β = 90
c = 175.51γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-11-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.9793SSRFBL17U

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
12.149.6358734

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 ENTRY 1o7a2.149.6158734587341000.217380.21738RANDOM37.479
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]
0.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.738
r_dihedral_angle_4_deg20.068
r_dihedral_angle_3_deg15.702
r_dihedral_angle_1_deg5.387
r_scangle_it1.811
r_scbond_it1.112
r_angle_refined_deg1.095
r_mcangle_it0.923
r_mcbond_it0.52
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.738
r_dihedral_angle_4_deg20.068
r_dihedral_angle_3_deg15.702
r_dihedral_angle_1_deg5.387
r_scangle_it1.811
r_scbond_it1.112
r_angle_refined_deg1.095
r_mcangle_it0.923
r_mcbond_it0.52
r_nbtor_refined0.304
r_nbd_refined0.19
r_symmetry_vdw_refined0.147
r_symmetry_hbond_refined0.12
r_xyhbond_nbd_refined0.118
r_chiral_restr0.079
r_bond_refined_d0.007
r_gen_planes_refined0.003
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
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 Atoms426
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
CNSrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing