☰ Navigation Tabs
Structure of HOXB13-DNA(TCG) complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XRM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 PEG 3350, potassium chloride, magnesium chloride, PEG 400, Tris
Crystal Properties Matthews coefficient Solvent content 3.55 65.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.618 α = 90 b = 52.522 β = 90 c = 389.331 γ = 90
Symmetry Space Group P 2 2 21
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 PSI PILATUS 6M 2014-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97239 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.2 46.29 93.7 0.097 6.7 4.4 17652
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 3.2 3.37 81.8 0.653 1.9 4.1
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 4XRM 3.2 46.29 16610 916 92.55 0.21934 0.21617 0.2154 0.2813 0.2788 RANDOM 120.992
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] -93.34 74.62 18.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.874 r_dihedral_angle_3_deg 25.618 r_long_range_B_refined 22.762 r_long_range_B_other 22.761 r_dihedral_angle_4_deg 19.886 r_mcangle_it 16.305 r_mcangle_other 16.298 r_scangle_other 14.812 r_mcbond_other 10.534 r_mcbond_it 10.526
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.874 r_dihedral_angle_3_deg 25.618 r_long_range_B_refined 22.762 r_long_range_B_other 22.761 r_dihedral_angle_4_deg 19.886 r_mcangle_it 16.305 r_mcangle_other 16.298 r_scangle_other 14.812 r_mcbond_other 10.534 r_mcbond_it 10.526 r_scbond_it 10.117 r_scbond_other 10.117 r_dihedral_angle_1_deg 7.295 r_angle_refined_deg 1.569 r_angle_other_deg 1.506 r_chiral_restr 0.133 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 2056 Nucleic Acid Atoms 3116 Solvent Atoms 17 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing