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Structure of the high affinity Anticalin P3D11 in complex with the human CD98 heavy chain ectodomain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DH2 2DH2, 4GH7 experimental model PDB 4GH7 2DH2, 4GH7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.75 293 18 % (w/v) PEG3350, 100 mM sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.23 44.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 202.809 α = 90 b = 46.052 β = 106.64 c = 137.092 γ = 90
Symmetry Space Group C 1 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 PILATUS3 2M 2017-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.8 30 99.8 0.045 0.049 1 23.86 6.781 113253 -3 37.366
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 99.9 0.865 0.934 0.833 2.32 7.038
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 2DH2, 4GH7 1.8 30 111018 2234 99.86 0.1853 0.1845 0.1967 0.2263 0.2315 RANDOM 34.081
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] 0.48 -0.35 0.56 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.15 r_dihedral_angle_4_deg 16.023 r_dihedral_angle_3_deg 13.253 r_dihedral_angle_1_deg 6.676 r_angle_refined_deg 1.755 r_angle_other_deg 1.057 r_chiral_restr 0.113 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.15 r_dihedral_angle_4_deg 16.023 r_dihedral_angle_3_deg 13.253 r_dihedral_angle_1_deg 6.676 r_angle_refined_deg 1.755 r_angle_other_deg 1.057 r_chiral_restr 0.113 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9248 Nucleic Acid Atoms Solvent Atoms 897 Heterogen Atoms 12
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing