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Endoglycosidase S in complex with IgG1 Fc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EN3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294.15 0.09 M halogens (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide), 0.1 M buffer system 2 (Sodium HEPES; MOPS (acid)), pH 7.5, 37.5 % v/v precipitant mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350) - condition B8 from Morpheus crystallisation screen (Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 3.2 61.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.529 α = 90 b = 174.294 β = 90 c = 193.059 γ = 90
Symmetry Space Group P 21 21 21
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 2022-05-28 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 3.45 49.78 100 0.144 0.15 0.04 1 11.2 13.7 43678
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 3.45 3.51 100 1.951 2.023 0.532 0.599 0.6 14.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6EN3 3.45 49.78 43613 2116 99.954 0.255 0.2525 0.2583 0.3112 0.3149 146.604
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] 2.654 2.667 -5.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 10.047 r_dihedral_angle_3_deg 9.905 r_lrange_it 8.76 r_lrange_other 8.76 r_mcangle_it 5.593 r_mcangle_other 5.593 r_dihedral_angle_1_deg 4.912 r_scangle_it 4.388 r_scangle_other 4.388 r_mcbond_it 3.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 10.047 r_dihedral_angle_3_deg 9.905 r_lrange_it 8.76 r_lrange_other 8.76 r_mcangle_it 5.593 r_mcangle_other 5.593 r_dihedral_angle_1_deg 4.912 r_scangle_it 4.388 r_scangle_other 4.388 r_mcbond_it 3.217 r_mcbond_other 3.217 r_scbond_it 2.402 r_scbond_other 2.402 r_dihedral_angle_2_deg 2.107 r_angle_refined_deg 0.604 r_angle_other_deg 0.234 r_symmetry_xyhbond_nbd_refined 0.179 r_symmetry_nbd_refined 0.167 r_nbtor_refined 0.165 r_symmetry_nbd_other 0.161 r_nbd_refined 0.159 r_nbd_other 0.146 r_xyhbond_nbd_refined 0.109 r_ncsr_local_group_1 0.087 r_symmetry_nbtor_other 0.075 r_ncsr_local_group_2 0.069 r_chiral_restr 0.028 r_chiral_restr_other 0.017 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16920 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling MOLREP phasing