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Complex structure of BANP BEN domain bound to 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 20% w/v PEG3350;
0.02 M Sodium/potassium phosphate;
0.1 M Bris-Tris propane pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.04 39.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.965 α = 90 b = 129.9 β = 90 c = 40.133 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 DECTRIS PILATUS3 6M 2022-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9791 SSRF BL18U1
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 2.11 50 99.9 0.086 0.998 17 12.4 11802
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 2.11 2.17 99.4 0.471 0.978 4.5 12.2
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 2.11 40.17 11149 615 99.91 0.2266 0.2246 0.2357 0.2618 0.2674 RANDOM 40.692
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] 5.88 -2.73 -3.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.423 r_dihedral_angle_3_deg 18.541 r_dihedral_angle_4_deg 15.266 r_dihedral_angle_1_deg 6.537 r_angle_refined_deg 1.482 r_angle_other_deg 1.414 r_chiral_restr 0.075 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.423 r_dihedral_angle_3_deg 18.541 r_dihedral_angle_4_deg 15.266 r_dihedral_angle_1_deg 6.537 r_angle_refined_deg 1.482 r_angle_other_deg 1.414 r_chiral_restr 0.075 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 949 Nucleic Acid Atoms 486 Solvent Atoms 55 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing