☰ Navigation Tabs
Structure of HOXB13 bound to hydroxymethylated DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EDN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 295 27% PEG 1000, 8% PEG 200, 0.15M KCl, 0.1M MgCl2, 0.05M Bis-Tris
Crystal Properties Matthews coefficient Solvent content 2.64 57.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.153 α = 88.02 b = 55.541 β = 81.46 c = 101.08 γ = 84.94
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 2018-07-23 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 1.97 48.85 97.2 0.284 0.326 0.158 0.97 2.4 4 55783
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 1.97 2.02 77.7 5.776 6.922 3.728 0.074 3.2
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 5EDN 2 47 52887 1603 98.64 0.2608 0.2601 0.2771 0.2831 0.3051 RANDOM 40.422
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] 1.88 -0.63 2.26 -1.05 -0.69 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.706 r_dihedral_angle_4_deg 19.023 r_dihedral_angle_3_deg 19.011 r_dihedral_angle_1_deg 5.191 r_angle_refined_deg 1.484 r_angle_other_deg 1.448 r_chiral_restr 0.076 r_gen_planes_refined 0.01 r_bond_refined_d 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.706 r_dihedral_angle_4_deg 19.023 r_dihedral_angle_3_deg 19.011 r_dihedral_angle_1_deg 5.191 r_angle_refined_deg 1.484 r_angle_other_deg 1.448 r_chiral_restr 0.076 r_gen_planes_refined 0.01 r_bond_refined_d 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2039 Nucleic Acid Atoms 2968 Solvent Atoms 356 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction