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Crystal structure of BAF60A (SMARCD1) apo containing partial coiled coil and the YEATS-like domain with topologically-linked SWIB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Alphafold2 model was used as an input in MrBUMP automated molecular replacement
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 20% w/v PEG3350, 0.2 M NH4NO3
Crystal Properties Matthews coefficient Solvent content 3.1 60.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.555 α = 90 b = 69.346 β = 120.47 c = 77.958 γ = 90
Symmetry Space Group C 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 PIXEL DECTRIS EIGER X 9M 2025-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98011 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.09 35.6 98.8 0.994 10.7 3.7 22251
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.14 0.858
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 2.09 35.58 21060 1186 98.47 0.21389 0.21086 0.2166 0.2658 0.266 RANDOM 49.013
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] 4.13 -3.35 2.51 -1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.265 r_dihedral_angle_3_deg 17.633 r_dihedral_angle_4_deg 13.436 r_long_range_B_refined 9.22 r_long_range_B_other 9.202 r_dihedral_angle_1_deg 7.088 r_scangle_other 6.932 r_mcangle_other 5.684 r_mcangle_it 5.68 r_scbond_it 4.704
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.265 r_dihedral_angle_3_deg 17.633 r_dihedral_angle_4_deg 13.436 r_long_range_B_refined 9.22 r_long_range_B_other 9.202 r_dihedral_angle_1_deg 7.088 r_scangle_other 6.932 r_mcangle_other 5.684 r_mcangle_it 5.68 r_scbond_it 4.704 r_scbond_other 4.703 r_mcbond_it 4.047 r_mcbond_other 4.034 r_angle_refined_deg 1.498 r_angle_other_deg 1.242 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 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 2007 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement PHASER phasing PDB_EXTRACT data extraction DIALS data reduction Aimless data scaling