4Q56

Structure of Helix aspersa agglutinin with natural glycosylation and N-acetyl-alpha-D-galactosamine (GalNAc)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CCVPDB entry 2CCV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72930.05 M Zn(CH3COO)2, 0.1 M HEPES, pH 7.0, 40% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7455.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.9α = 90
b = 47.9β = 90
c = 281.53γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6Mmirrors2013-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.967PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.3846.921000.03429.3510.542529425294-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.381.481000.01142.5410.3

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 2CCV1.3846.922529425294108399.950.137880.136580.16782RANDOM31.068
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]
0.590.590.59-1.93
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free29.808
r_dihedral_angle_2_deg27.939
r_dihedral_angle_4_deg22.175
r_sphericity_bonded14.734
r_dihedral_angle_3_deg12.463
r_long_range_B_refined6.834
r_dihedral_angle_1_deg6.557
r_scangle_other5.397
r_long_range_B_other5.301
r_rigid_bond_restr5.082
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free29.808
r_dihedral_angle_2_deg27.939
r_dihedral_angle_4_deg22.175
r_sphericity_bonded14.734
r_dihedral_angle_3_deg12.463
r_long_range_B_refined6.834
r_dihedral_angle_1_deg6.557
r_scangle_other5.397
r_long_range_B_other5.301
r_rigid_bond_restr5.082
r_scbond_other4.835
r_scbond_it4.431
r_mcangle_other4.145
r_mcangle_it3.61
r_mcbond_it2.936
r_mcbond_other2.897
r_angle_refined_deg2.013
r_angle_other_deg0.876
r_chiral_restr0.121
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms796
Nucleic Acid Atoms
Solvent Atoms119
Heterogen Atoms91

Software

Software
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
REFMACrefinement