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Crystal structure of human BEND6 BEN domain in complex with methylated DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YUK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1 M carboxylic acids, 0.1 M imidazole, 0.1 M MES monohydrate (acid) (pH 6.5), 12.5% MPD (v/v), 12.5 % PEG 1000 (v/v), and 12.5% PEG 3350 (w/v).
Crystal Properties Matthews coefficient Solvent content 2.24 45.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.482 α = 90 b = 67.276 β = 100.72 c = 53.019 γ = 90
Symmetry Space Group P 1 21 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 Bruker PHOTON III 2022-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE BRUKER METALJET 1.34138
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 2.13 34.34 99.9 0.0559 17.36 4.77 15367
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 2.13 2.16 99.8 0.2398 4.5 3.14
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 7YUK 2.13 34.34 14571 780 99.94 0.18694 0.18447 0.1924 0.23356 0.2426 RANDOM 24.344
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] 0.01 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.461 r_dihedral_angle_4_deg 18.259 r_dihedral_angle_3_deg 15.603 r_dihedral_angle_1_deg 6.66 r_long_range_B_refined 5.429 r_long_range_B_other 5.337 r_scangle_other 3.779 r_mcangle_it 2.799 r_mcangle_other 2.798 r_scbond_it 2.437
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.461 r_dihedral_angle_4_deg 18.259 r_dihedral_angle_3_deg 15.603 r_dihedral_angle_1_deg 6.66 r_long_range_B_refined 5.429 r_long_range_B_other 5.337 r_scangle_other 3.779 r_mcangle_it 2.799 r_mcangle_other 2.798 r_scbond_it 2.437 r_scbond_other 2.437 r_mcbond_it 1.854 r_mcbond_other 1.851 r_angle_refined_deg 1.647 r_angle_other_deg 1.386 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 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 1465 Nucleic Acid Atoms 488 Solvent Atoms 155 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SAINT data scaling SAINT data reduction PDB_EXTRACT data extraction PHASER phasing