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Endoglycosidase S2 in complex with IgG1 Fc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6E58 experimental model PDB 3AVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 Morpheus (Molecular Dimensions) conditon G12:
0.1 M carboxylic acids(0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Potassium sodium tartrate tetrahydrate; 0.2M Sodium oxamate); 0.1 M buffer system 3(Tris (base); BICINE); pH 8.5; 37.5 v/v Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)
Crystal Properties Matthews coefficient Solvent content 2.98 58.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 228.775 α = 90 b = 228.775 β = 90 c = 161.629 γ = 90
Symmetry Space Group P 43 21 2
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 EIGER2 XE 16M 2023-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 3 49.91 100 0.187 0.191 0.036 1 12.6 27.5 85926 77
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.05 100 2.614 2.668 0.527 0.64 0.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3 49.91 85849 4376 99.956 0.218 0.2161 0.22 0.2516 0.2563 100.098
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] -0.691 -0.691 1.382
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.787 r_dihedral_angle_6_deg 13.837 r_dihedral_angle_2_deg 6.77 r_dihedral_angle_1_deg 6.462 r_lrange_it 6.25 r_lrange_other 6.244 r_scangle_it 2.648 r_scangle_other 2.648 r_mcangle_it 2.428 r_mcangle_other 2.428
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.787 r_dihedral_angle_6_deg 13.837 r_dihedral_angle_2_deg 6.77 r_dihedral_angle_1_deg 6.462 r_lrange_it 6.25 r_lrange_other 6.244 r_scangle_it 2.648 r_scangle_other 2.648 r_mcangle_it 2.428 r_mcangle_other 2.428 r_scbond_it 1.496 r_scbond_other 1.496 r_mcbond_it 1.41 r_mcbond_other 1.41 r_angle_refined_deg 0.957 r_angle_other_deg 0.526 r_xyhbond_nbd_refined 0.203 r_symmetry_nbd_other 0.195 r_nbd_refined 0.182 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.169 r_symmetry_nbd_refined 0.167 r_nbd_other 0.16 r_metal_ion_refined 0.11 r_ncsr_local_group_1 0.108 r_ncsr_local_group_2 0.104 r_ncsr_local_group_5 0.104 r_ncsr_local_group_6 0.1 r_ncsr_local_group_3 0.095 r_ncsr_local_group_4 0.09 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.059 r_symmetry_xyhbond_nbd_other 0.024 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20629 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 258
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling MOLREP phasing