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Structure of Sox17 Bound to DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GT0 PDB ENTRY 1GT0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 30% PEG 3350, 0.2M MGCL2, pH 7.4, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.28 45.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.753 α = 90 b = 68.753 β = 90 c = 66.329 γ = 120
Symmetry Space Group P 32 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 IMAGE PLATE RIGAKU RAXIS Platinum SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.75 66.33 99.9 0.069 22.75 9.86 4970
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 2.75 2.85 0.387 3.75 7.6
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 PDB ENTRY 1GT0 2.75 20.73 4703 228 99.46 0.243 0.242 0.2314 0.265 0.2589 RANDOM 25.696
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] 2.25 1.13 2.25 -3.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.735 r_dihedral_angle_4_deg 27.49 r_dihedral_angle_3_deg 21.173 r_dihedral_angle_1_deg 4.808 r_scangle_it 1.977 r_angle_refined_deg 1.861 r_scbond_it 1.262 r_mcangle_it 1.004 r_mcbond_it 0.562 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.735 r_dihedral_angle_4_deg 27.49 r_dihedral_angle_3_deg 21.173 r_dihedral_angle_1_deg 4.808 r_scangle_it 1.977 r_angle_refined_deg 1.861 r_scbond_it 1.262 r_mcangle_it 1.004 r_mcbond_it 0.562 r_nbtor_refined 0.31 r_nbd_refined 0.246 r_symmetry_vdw_refined 0.225 r_symmetry_hbond_refined 0.214 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 633 Nucleic Acid Atoms 650 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose SAINT data scaling REFMAC refinement PDB_EXTRACT data extraction