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Structure of the AT-Hook 1 peptide from the mammalian HMGA protein in complex with DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EIL Chains A and B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 277.15 Crystallization buffer:
0.025mM NiCl2
10 mM MgCl2
2.5% MPD
25 mM NaCaco, pH 6
Final well concentration MPD about 38%
Crystallization drops were setup at 285.15 K, using a well solution consisting of aqueous MPD at 17% (v/v) concentration. After three days, the temperature was lowererd to 281.15 K. After 3 days at 281.15K, the solution in the well solution was changed to 25% MPD in water. After 1 week, the temperature was changed to 277.15K. The well solution was interchanged to a MPD solution at 30%. and after 8 days it was replaced by a 38% (v/v) MPD solution.
Crystal Properties Matthews coefficient Solvent content 2.28 46.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.635 α = 90 b = 43.635 β = 90 c = 97.48 γ = 120
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 PILATUS 6M KB mirrors, Si surface 2017-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97925 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.4 37.79 99.8 0.067 0.072 0.025 0.998 18.5 8.4 40810 -3
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 1.4 1.424 0.579 0.619 0.326 0.922 3.9
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 1.4 37.79 38850 1975 99.81 0.12597 0.12424 0.1286 0.15812 0.1595 RANDOM 14.952
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] -0.52 -0.26 -0.52 1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 17.447 r_dihedral_angle_3_deg 12.344 r_dihedral_angle_1_deg 7.548 r_dihedral_angle_2_deg 3.857 r_long_range_B_refined 2.978 r_long_range_B_other 2.73 r_scangle_other 2.725 r_scbond_it 1.893 r_scbond_other 1.891 r_mcangle_it 1.835
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 17.447 r_dihedral_angle_3_deg 12.344 r_dihedral_angle_1_deg 7.548 r_dihedral_angle_2_deg 3.857 r_long_range_B_refined 2.978 r_long_range_B_other 2.73 r_scangle_other 2.725 r_scbond_it 1.893 r_scbond_other 1.891 r_mcangle_it 1.835 r_mcangle_other 1.826 r_rigid_bond_restr 1.815 r_angle_other_deg 1.605 r_angle_refined_deg 1.58 r_mcbond_it 1.405 r_mcbond_other 1.372 r_chiral_restr 0.069 r_gen_planes_refined 0.029 r_bond_refined_d 0.007 r_gen_planes_other 0.004 r_bond_other_d 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 167 Nucleic Acid Atoms 1426 Solvent Atoms 361 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction pointless data scaling PHASER phasing