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TWIST1-TCF4-ALX4 complex on specific DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6OD3 experimental model PDB 2M0C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 Sodium Cacodylate buffer (pH 7.5),
100 mM magnesium acetate,
18 % Glycerol,
20 % 2-Methyl-2,4-pentanediol,
6-7% PEG (Mw 8000)
Crystal Properties Matthews coefficient Solvent content 3.29 62.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.589 α = 90 b = 60.589 β = 90 c = 237.289 γ = 120
Symmetry Space Group P 31 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 PIXEL DECTRIS PILATUS 6M 2022-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 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 2.82 47.99 97.9 0.212 0.223 0.068 0.995 8 10.4 12686
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 2.82 2.98 86.4 4.877 5.126 1.546 0.149 10.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.9 47 11318 598 99.81 0.22251 0.21968 0.2248 0.26987 0.273 RANDOM 88.448
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] 1.08 0.54 1.08 -3.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.671 r_dihedral_angle_3_deg 24.222 r_dihedral_angle_4_deg 22.597 r_long_range_B_refined 16.646 r_long_range_B_other 16.643 r_scangle_other 13.049 r_mcangle_it 11.738 r_mcangle_other 11.733 r_scbond_it 8.531 r_scbond_other 8.522
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.671 r_dihedral_angle_3_deg 24.222 r_dihedral_angle_4_deg 22.597 r_long_range_B_refined 16.646 r_long_range_B_other 16.643 r_scangle_other 13.049 r_mcangle_it 11.738 r_mcangle_other 11.733 r_scbond_it 8.531 r_scbond_other 8.522 r_mcbond_it 7.955 r_mcbond_other 7.952 r_dihedral_angle_1_deg 7.642 r_angle_refined_deg 1.965 r_angle_other_deg 1.14 r_chiral_restr 0.167 r_gen_planes_refined 0.009 r_bond_refined_d 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 1592 Nucleic Acid Atoms 1025 Solvent Atoms 27 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing