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Structure of Helix aspersa agglutinin with natural glycosylation and N-acetyl-alpha-D-galactosamine (GalNAc)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CCV PDB entry 2CCV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.05 M Zn(CH3COO)2, 0.1 M HEPES, pH 7.0, 40% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.74 55.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.9 α = 90 b = 47.9 β = 90 c = 281.53 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M mirrors 2013-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.967 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.38 46.92 100 0.034 29.35 10.54 25294 25294 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.38 1.48 100 0.0114 2.54 10.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2CCV 1.38 46.92 25294 25294 1083 99.95 0.13788 0.13658 0.1405 0.16782 0.1701 RANDOM 31.068
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] 0.59 0.59 0.59 -1.93
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 29.808 r_dihedral_angle_2_deg 27.939 r_dihedral_angle_4_deg 22.175 r_sphericity_bonded 14.734 r_dihedral_angle_3_deg 12.463 r_long_range_B_refined 6.834 r_dihedral_angle_1_deg 6.557 r_scangle_other 5.397 r_long_range_B_other 5.301 r_rigid_bond_restr 5.082
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 29.808 r_dihedral_angle_2_deg 27.939 r_dihedral_angle_4_deg 22.175 r_sphericity_bonded 14.734 r_dihedral_angle_3_deg 12.463 r_long_range_B_refined 6.834 r_dihedral_angle_1_deg 6.557 r_scangle_other 5.397 r_long_range_B_other 5.301 r_rigid_bond_restr 5.082 r_scbond_other 4.835 r_scbond_it 4.431 r_mcangle_other 4.145 r_mcangle_it 3.61 r_mcbond_it 2.936 r_mcbond_other 2.897 r_angle_refined_deg 2.013 r_angle_other_deg 0.876 r_chiral_restr 0.121 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 796 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 91
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing REFMAC refinement