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IdeS in complex with IgG1 Fc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y08
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 294.15 0.12 M monosaccharides mix (0.2M D-Glucose; 0.2M D-Mannose; 0.2M D-Galactose; 0.2M L-Fucose; 0.2M D- Xylose; 0.2M N-Acetyl-D-Glucosamine), 0.1 M buffer system 3 (Tris (base); BICINE; pH 8.5), 30 % v/v precipitant mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000)
Crystal Properties Matthews coefficient Solvent content 4.08 69.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 217.558 α = 90 b = 108.448 β = 90.059 c = 63.093 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER X 4M Vertical CRL 2021-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.338 48.53 97.7 0.229 0.255 0.112 5.3 4.96 60351
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 2.34 2.38 98.8 0.877 0.978 0.426 0.335 1 5
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 1Y08 2.338 48.529 60350 3049 97.398 0.173 0.1712 0.1605 0.2031 0.1924 36.18
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] 0.77 -1.549 8.708 -9.478
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.924 r_dihedral_angle_3_deg 15.053 r_dihedral_angle_1_deg 7.671 r_lrange_it 7.108 r_lrange_other 7.108 r_dihedral_angle_2_deg 6.497 r_scangle_it 5.195 r_scangle_other 5.195 r_mcangle_it 4.876 r_mcangle_other 4.875
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.924 r_dihedral_angle_3_deg 15.053 r_dihedral_angle_1_deg 7.671 r_lrange_it 7.108 r_lrange_other 7.108 r_dihedral_angle_2_deg 6.497 r_scangle_it 5.195 r_scangle_other 5.195 r_mcangle_it 4.876 r_mcangle_other 4.875 r_scbond_it 3.568 r_scbond_other 3.568 r_mcbond_it 3.434 r_mcbond_other 3.431 r_angle_refined_deg 1.448 r_angle_other_deg 0.499 r_symmetry_nbd_refined 0.313 r_nbd_refined 0.197 r_symmetry_xyhbond_nbd_refined 0.195 r_symmetry_nbd_other 0.194 r_xyhbond_nbd_refined 0.183 r_nbtor_refined 0.178 r_nbd_other 0.176 r_ncsr_local_group_1 0.131 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.078 r_chiral_restr 0.07 r_chiral_restr_other 0.016 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5791 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 185
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling MOLREP phasing