☰ Navigation Tabs
Crystal structure of human BEND6 BEN domain in complex with DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YUG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.12 M Ethylene glycol, 0.1 M Sodium HEPES, 0.1 M MOPS (acid), 12.5% MPD (v/v), 12.5% PEG 1000 (v/v), 12.5% PEG3350 (v/v)
Crystal Properties Matthews coefficient Solvent content 1.94 36.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.092 α = 90 b = 39.514 β = 90 c = 43.719 γ = 90
Symmetry Space Group P 21 21 2
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 1.82 27.11 99.4 0.0451 34.15 7.69 11195
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 1.82 1.85 92.7 0.159 9.77 3.26
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 7YUG 1.82 27.11 10599 567 99.37 0.1594 0.1575 0.1692 0.1943 0.2013 RANDOM 16.862
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] -0.04 0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.544 r_dihedral_angle_4_deg 15.154 r_dihedral_angle_3_deg 13.785 r_dihedral_angle_1_deg 6.303 r_angle_refined_deg 1.826 r_angle_other_deg 1.488 r_chiral_restr 0.098 r_gen_planes_refined 0.013 r_bond_refined_d 0.011 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.544 r_dihedral_angle_4_deg 15.154 r_dihedral_angle_3_deg 13.785 r_dihedral_angle_1_deg 6.303 r_angle_refined_deg 1.826 r_angle_other_deg 1.488 r_chiral_restr 0.098 r_gen_planes_refined 0.013 r_bond_refined_d 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 737 Nucleic Acid Atoms 243 Solvent Atoms 140 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SAINT data scaling PDB_EXTRACT data extraction PHASER phasing