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Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TGATGAGCAG and loaded with Even-skipped homeodomain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7RVA experimental model PDB 1JGG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 40mM Magnesium acetate, 1.4M Lithium sulfate, 50mM MES pH 6.5. The crystal was crosslinked with 33mg/mL EDC overnight, and then looped into a solution of 25mM potassium chloride, 4mM calcium chloride, 10% glycerol, and 10mM Tris hydrochloride for 1 hour. The drop was then supplemented with 30 micromolar Even-skipped homeodomain.
Crystal Properties Matthews coefficient Solvent content 5.04 75.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.032 α = 90 b = 124.855 β = 91.846 c = 139.093 γ = 90
Symmetry Space Group I 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 EIGER X 9M 2025-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.04 47.23 98.7 0.077 0.092 0.049 0.999 10.5 3.5 23358 93.44
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 3.04 3.25 99.4 0.819 0.962 0.501 0.863 1.6 3.6
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 3.16 46.8 1.34 21733 2166 97.42 0.2639 0.2618 0.2616 0.2827 0.2819 117.65
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 23.234 f_angle_d 0.4774 f_chiral_restr 0.0348 f_plane_restr 0.0045 f_bond_d 0.0028
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2421 Nucleic Acid Atoms 1271 Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building