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X-Ray structure of F240L mutant HOXB13 in complex with DNA (CAA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EEA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 24% PEG3350, 150mM KCl, 100mM MgCl2, Tris pH8.0
Crystal Properties Matthews coefficient Solvent content 2.39 48.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.22 α = 90 b = 57.82 β = 119 c = 75.49 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 EIGER2 XE 16M 2024-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 35.83 98.3 1 15.5 7 30715 42.48
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 98.4 0.712 1.3 7
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 1.95 33.01 1.34 30609 1560 97.8 0.2284 0.2261 0.2184 0.2734 0.2635 48.59
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 30.7189 f_angle_d 0.9177 f_chiral_restr 0.0414 f_bond_d 0.0075 f_plane_restr 0.0052
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 956 Nucleic Acid Atoms 1464 Solvent Atoms 131 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing