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Oct4/Sox2 protein:DNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HT5 6ht5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.1M HEPES, 70% (v/v) MPD
Crystal Properties Matthews coefficient Solvent content 3.68 66.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.169 α = 90 b = 163.169 β = 90 c = 39.792 γ = 120
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 EIGER X 16M 2020-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97624 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.137 81.585 77.4 0.114 0.996 14.8 19.5 8506
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.137 3.342 22.7 2.135 0.548 1.6 18.4
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 6ht5 3.14 81.72 8135 368 77.48 0.20075 0.19861 0.1974 0.25234 0.252 RANDOM 144.695
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] 1.5 0.75 1.5 -4.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.133 r_long_range_B_refined 28.635 r_dihedral_angle_4_deg 19.878 r_dihedral_angle_3_deg 19.764 r_mcangle_it 19.059 r_scbond_it 15.027 r_mcbond_it 13.128 r_dihedral_angle_1_deg 5.676 r_angle_refined_deg 2.508 r_chiral_restr 0.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.133 r_long_range_B_refined 28.635 r_dihedral_angle_4_deg 19.878 r_dihedral_angle_3_deg 19.764 r_mcangle_it 19.059 r_scbond_it 15.027 r_mcbond_it 13.128 r_dihedral_angle_1_deg 5.676 r_angle_refined_deg 2.508 r_chiral_restr 0.219 r_gen_planes_refined 0.013 r_bond_refined_d 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1396 Nucleic Acid Atoms 902 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling STARANISO data scaling MOLREP phasing