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X-ray crystallographic structure of a high affinity IGF2 antagonist (Domain11 AB5 RHH) based on human IGF2R domain 11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GP0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 2.0 M Ammonium Sulphate, 0.1M Bis-(2-hydroxyethyl)imino-tris(hydroxymethyl methane, pH 7.0.
Crystal Properties Matthews coefficient Solvent content 2.06 40.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.12 α = 90 b = 48.56 β = 90 c = 62.55 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 300K 2015-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.8 38.36 99.8 0.2 0.989 6.4 6.2 3414 26.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.86 100 1.2 1.35 6.4
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 1GP0 2.8 38.36 3063 351 99.8 0.22479 0.22198 0.2374 0.24908 0.2562 RANDOM 26.441
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] 3.52 -2.92 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.872 r_dihedral_angle_3_deg 15.977 r_dihedral_angle_4_deg 15.755 r_dihedral_angle_1_deg 6.546 r_long_range_B_other 3.988 r_long_range_B_refined 3.986 r_scangle_other 2.716 r_mcangle_it 2.242 r_mcangle_other 2.241 r_angle_refined_deg 1.745
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.872 r_dihedral_angle_3_deg 15.977 r_dihedral_angle_4_deg 15.755 r_dihedral_angle_1_deg 6.546 r_long_range_B_other 3.988 r_long_range_B_refined 3.986 r_scangle_other 2.716 r_mcangle_it 2.242 r_mcangle_other 2.241 r_angle_refined_deg 1.745 r_scbond_other 1.602 r_scbond_it 1.601 r_mcbond_it 1.283 r_mcbond_other 1.283 r_angle_other_deg 1.029 r_chiral_restr 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1018 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing