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COMPLEX STRUCTURE OF CD93-IGFBP7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Predicted CD93 domains were used for MR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1 M imidazole, 20% w/v PEG monomethyl ether 2000, and 0.2 M ammonium citrate tribasic pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.31 62.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.512 α = 90 b = 208.895 β = 90 c = 77.58 γ = 90
Symmetry Space Group C 2 2 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 2022-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.9790 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3.24 48.2 99.9 0.2 0.2 0.2 0.09 0.996 9.4 12 17340 118.44
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 3.24 3.5 99.9 2.14 1 0.48 1.3 10.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.24 19.95 1.34 17248 849 99.83 0.2464 0.2437 0.2436 0.3018 0.3024 143.97
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.4984 f_angle_d 0.464 f_chiral_restr 0.0371 f_plane_restr 0.0055 f_bond_d 0.0019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5364 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction XDS data scaling PHENIX phasing