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Crystal structure of the complex between Neuronal Pentraxin 2 (NP2 PTX) and antibody fragment VHH N1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 1% w/v tryptone, 0.001 M sodium azide, 0.05 M HEPES sodium pH7.0, 12% w/v PEG 3,350.
Crystal Properties Matthews coefficient Solvent content 2.85 56.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.574 α = 90 b = 118.234 β = 90 c = 39.464 γ = 90
Symmetry Space Group P 21 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 PILATUS3 S 6M 2024-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.02 46.8 98.2 0.066 0.029 1 31.7 12.5 29010
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.02 2.07 80.8 1.051 0.353 0.782 2.4 9.4
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 THROUGHOUT 2.02 46.8 28961 1428 97.858 0.183 0.1816 0.1893 0.2197 0.2278 44.103
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] 1.384 1.785 -3.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.032 r_dihedral_angle_3_deg 13.33 r_dihedral_angle_2_deg 10.082 r_dihedral_angle_1_deg 7.802 r_lrange_other 6.732 r_lrange_it 6.728 r_scangle_it 4.797 r_scangle_other 4.796 r_mcangle_it 3.568 r_mcangle_other 3.568
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.032 r_dihedral_angle_3_deg 13.33 r_dihedral_angle_2_deg 10.082 r_dihedral_angle_1_deg 7.802 r_lrange_other 6.732 r_lrange_it 6.728 r_scangle_it 4.797 r_scangle_other 4.796 r_mcangle_it 3.568 r_mcangle_other 3.568 r_scbond_it 3.27 r_scbond_other 3.269 r_mcbond_it 2.531 r_mcbond_other 2.526 r_angle_refined_deg 1.618 r_angle_other_deg 0.548 r_xyhbond_nbd_refined 0.243 r_symmetry_metal_ion_refined 0.23 r_nbd_refined 0.212 r_symmetry_nbd_refined 0.202 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.185 r_nbd_other 0.169 r_metal_ion_refined 0.137 r_symmetry_xyhbond_nbd_refined 0.132 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.073 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2543 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing