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Complex of the Nanofitin Sac7d-C3(C24A) with a human IgG1 Fc fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XIW experimental model PDB 1L6X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 24 % (w/v) PEG8000, 0.1 M Tris/HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.6 52.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.27 α = 90 b = 136.84 β = 90.12 c = 69.76 γ = 90
Symmetry Space Group P 1 21 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 16M 2024-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97620 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.9 136.8 97 0.099 0.119 0.994 7.74 3.1 27577
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 0.748 0.902 0.676
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.9 69.76 26198 1379 97.02 0.22991 0.22729 0.27928 0.2894 RANDOM 87.216
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] -5.23 -0.99 -1.91 7.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.34 r_long_range_B_refined 11.266 r_long_range_B_other 11.266 r_dihedral_angle_2_deg 10.02 r_dihedral_angle_1_deg 7.275 r_mcangle_it 6.459 r_mcangle_other 6.459 r_scangle_other 5.897 r_mcbond_it 3.862 r_mcbond_other 3.862
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.34 r_long_range_B_refined 11.266 r_long_range_B_other 11.266 r_dihedral_angle_2_deg 10.02 r_dihedral_angle_1_deg 7.275 r_mcangle_it 6.459 r_mcangle_other 6.459 r_scangle_other 5.897 r_mcbond_it 3.862 r_mcbond_other 3.862 r_scbond_it 3.434 r_scbond_other 3.434 r_angle_refined_deg 1.443 r_angle_other_deg 0.481 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8892 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PHASER phasing