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Engineered scFv 10LH bound to PHOX2B/HLA-A24:02
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7MJA 7MJA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 20% PEG 3350, 0.2M Sodium Nitrate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.087 α = 90 b = 174.562 β = 118.75 c = 47.193 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 PILATUS 6M 2022-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.108 43.68 97.4 0.095 0.111 0.057 0.995 4.5 3.8 37369
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 2.108 2.115 98.7 0.644 0.776 0.389 0.817 2.2 3.7
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7MJA 2.11 43.68 35362 2006 97.37 0.18319 0.18149 0.1904 0.21245 0.2168 RANDOM 35.173
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] 2.91 0.44 -2.16 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.392 r_dihedral_angle_4_deg 16.464 r_dihedral_angle_3_deg 14.625 r_dihedral_angle_1_deg 6.247 r_long_range_B_refined 4.465 r_long_range_B_other 4.314 r_scangle_other 1.901 r_mcangle_it 1.607 r_mcangle_other 1.607 r_angle_refined_deg 1.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.392 r_dihedral_angle_4_deg 16.464 r_dihedral_angle_3_deg 14.625 r_dihedral_angle_1_deg 6.247 r_long_range_B_refined 4.465 r_long_range_B_other 4.314 r_scangle_other 1.901 r_mcangle_it 1.607 r_mcangle_other 1.607 r_angle_refined_deg 1.296 r_scbond_it 1.186 r_scbond_other 1.174 r_angle_other_deg 1.026 r_mcbond_it 0.974 r_mcbond_other 0.974 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4857 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHENIX phasing