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Structure of the ultra-affinity complex between CFH and a nanobody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SW0 3SW0, 5LHN experimental model PDB 5LHN 3SW0, 5LHN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Sodium Phosphate monohydrate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.21 61.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.96 α = 90 b = 75.96 β = 90 c = 143.2 γ = 120
Symmetry Space Group P 32 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 PILATUS3 S 2M 2020-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.6 48.44 99.9 0.16 0.997 12.3 13.5 15303
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.74 0.916 2.6
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 3SW0, 5LHN 2.6 48.44 15281 753 99.876 0.194 0.1921 0.1997 0.2392 0.2391 62.83
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] 1.925 0.962 1.925 -6.245
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.987 r_dihedral_angle_4_deg 23.3 r_dihedral_angle_3_deg 18.402 r_dihedral_angle_1_deg 8.689 r_lrange_it 7.154 r_lrange_other 7.152 r_scangle_it 5.572 r_scangle_other 5.571 r_mcangle_other 4.349 r_mcangle_it 4.345
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.987 r_dihedral_angle_4_deg 23.3 r_dihedral_angle_3_deg 18.402 r_dihedral_angle_1_deg 8.689 r_lrange_it 7.154 r_lrange_other 7.152 r_scangle_it 5.572 r_scangle_other 5.571 r_mcangle_other 4.349 r_mcangle_it 4.345 r_scbond_it 3.623 r_scbond_other 3.622 r_mcbond_it 2.82 r_mcbond_other 2.79 r_angle_refined_deg 1.863 r_angle_other_deg 1.345 r_symmetry_xyhbond_nbd_refined 0.224 r_nbd_refined 0.212 r_nbd_other 0.197 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.181 r_symmetry_nbd_refined 0.158 r_xyhbond_nbd_refined 0.152 r_symmetry_xyhbond_nbd_other 0.092 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.074 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1985 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing