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Structure of the high affinity engineered lipocalin C1B12 in complex with the mouse CD98 heavy chain ectodomain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6I9Q 6I9Q, 6S8V experimental model PDB 6S8V 6I9Q, 6S8V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 12 %(w/v) PEG8000, 0.2 M Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.71 54.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.039 α = 90 b = 107.737 β = 90 c = 133.872 γ = 90
Symmetry Space Group P 21 21 2
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 2018-03-22 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 2.75 34.71 99.1 0.197 0.205 0.996 15.36 13.198 39856 42.73
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 2.75 2.85 96.6 1.079 1.128 0.769 2.45 11.718
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 6I9Q, 6S8V 2.75 34.71 37895 1961 99.09 0.2222 0.2197 0.2235 0.2709 0.2718 RANDOM 43.758
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] -0.85 -3.22 4.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.391 r_dihedral_angle_4_deg 14.819 r_dihedral_angle_3_deg 14.552 r_dihedral_angle_1_deg 6.297 r_angle_refined_deg 1.182 r_angle_other_deg 1.068 r_chiral_restr 0.039 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.391 r_dihedral_angle_4_deg 14.819 r_dihedral_angle_3_deg 14.552 r_dihedral_angle_1_deg 6.297 r_angle_refined_deg 1.182 r_angle_other_deg 1.068 r_chiral_restr 0.039 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9424 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing