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Crystal structure of PILRA in complex with Fab portion of antagonist antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WUZ experimental model Other internal Fab crystal structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1 M CAPS pH 10.5, 20% PEG 8000, 0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.27 45.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.854 α = 90 b = 46.753 β = 90 c = 335.052 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 EIGER X 16M 2025-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.97946 SSRL BL12-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.579 46.347 92.3 0.986 5.2 2.6 18280
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 2.58 2.72 86.6 0.301
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 FREE R-VALUE 2.579 46.347 18146 888 91.443 0.229 0.2261 0.2271 0.2774 0.2767 55.522
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] -1.141 1.463 -0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.329 r_dihedral_angle_6_deg 14.377 r_dihedral_angle_2_deg 10.513 r_lrange_it 8.712 r_dihedral_angle_1_deg 7.324 r_scangle_it 5.385 r_mcangle_it 4.177 r_scbond_it 3.494 r_mcbond_it 2.551 r_angle_refined_deg 1.594
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.329 r_dihedral_angle_6_deg 14.377 r_dihedral_angle_2_deg 10.513 r_lrange_it 8.712 r_dihedral_angle_1_deg 7.324 r_scangle_it 5.385 r_mcangle_it 4.177 r_scbond_it 3.494 r_mcbond_it 2.551 r_angle_refined_deg 1.594 r_nbtor_refined 0.304 r_symmetry_xyhbond_nbd_refined 0.269 r_symmetry_nbd_refined 0.239 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.098 r_bond_refined_d 0.006 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4315 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing