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sc-4E (scFv derived from the mAb 4E1 against CD93) crystallized at pH 7.5 (monomeric state from gel filtration)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DET
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 4.1 M NaCl, 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.19 61.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.42 α = 90 b = 64.42 β = 90 c = 161.124 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 EIGER X 16M 2024-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97630 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) 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 1.7 40.28 99.9 0.074 0.076 0.017 0.999 20.7 19.9 43566 34.8
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 1.7 1.73 100 1.87 1.917 0.418 0.437 2.1 20.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.7 32.21 41143 2283 99.71 0.17837 0.17656 0.1779 0.21148 0.211 RANDOM 39.945
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.98 r_dihedral_angle_1_deg 7.292 r_long_range_B_refined 7.095 r_dihedral_angle_2_deg 5.49 r_scbond_it 3.96 r_mcangle_it 3.713 r_mcbond_it 2.904 r_angle_refined_deg 2.131 r_chiral_restr 0.159 r_gen_planes_refined 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.98 r_dihedral_angle_1_deg 7.292 r_long_range_B_refined 7.095 r_dihedral_angle_2_deg 5.49 r_scbond_it 3.96 r_mcangle_it 3.713 r_mcbond_it 2.904 r_angle_refined_deg 2.131 r_chiral_restr 0.159 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1760 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing