☰ Navigation Tabs
TEAD4-HOXB13 complex bound to DNA
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 7.24 298 PEG (4000), Ammonium sulphate, PME(550, MOPs
Crystal Properties Matthews coefficient Solvent content 3.13 60.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.659 α = 90 b = 56.674 β = 93.81 c = 144.993 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 CCD ADSC QUANTUM 315r 2016-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97242 ESRF ID23-1
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 2.88 46.71 95.1 0.039 0.049 0.029 1 12 2.4 14626
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 2.88 3.06 94.8 1.845 2.288 1.331 0.257 2.4
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 5EEA 2.88 45 13860 765 95.04 0.24371 0.23955 0.241 0.31677 0.3181 RANDOM 125.688
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] 2.99 3.45 1.42 -4.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.051 r_dihedral_angle_1_deg 29.575 r_dihedral_angle_3_deg 22.732 r_long_range_B_refined 16.968 r_long_range_B_other 16.968 r_dihedral_angle_4_deg 14.822 r_mcangle_it 14.274 r_mcangle_other 14.268 r_scangle_other 11.776 r_mcbond_it 8.836
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.051 r_dihedral_angle_1_deg 29.575 r_dihedral_angle_3_deg 22.732 r_long_range_B_refined 16.968 r_long_range_B_other 16.968 r_dihedral_angle_4_deg 14.822 r_mcangle_it 14.274 r_mcangle_other 14.268 r_scangle_other 11.776 r_mcbond_it 8.836 r_mcbond_other 8.821 r_scbond_it 7.536 r_scbond_other 7.532 r_angle_refined_deg 1.459 r_angle_other_deg 1.307 r_chiral_restr 0.258 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.003 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 2230 Nucleic Acid Atoms 1476 Solvent Atoms 16 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction