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Recognition of different base tetrads by RHAU: X-ray crystal structure of G4 recognition motif bound to the 3-end tetrad of a DNA G-quadruplex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2LK7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 55% methylpentanediol, 40 mM sodium cacodylate (pH 6.0), 80 mM potassium chloride and 12 mM spermine tetrahydrochloride
Crystal Properties Matthews coefficient Solvent content 2.11 41.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.39 α = 90 b = 42.25 β = 99.3 c = 61.404 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 DECTRIS PILATUS 2M-F 2016-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.5 60.6 99.35 0.079 0.998 8.68 3.827 45681
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.59 98.3 0.763 0.816 1.62 3.62
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 2LK7 1.5 60.6 43297 2308 99.35 0.18832 0.1853 0.1919 0.24481 0.2473 RANDOM 26.597
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] 0.71 -0.4 -0.47 -0.1
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.931 r_dihedral_angle_2_deg 25.901 r_sphericity_bonded 20.311 r_dihedral_angle_3_deg 18.268 r_dihedral_angle_4_deg 9.038 r_dihedral_angle_1_deg 7.104 r_long_range_B_refined 6.713 r_mcangle_it 6.596 r_mcangle_other 6.587 r_long_range_B_other 6.411
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.931 r_dihedral_angle_2_deg 25.901 r_sphericity_bonded 20.311 r_dihedral_angle_3_deg 18.268 r_dihedral_angle_4_deg 9.038 r_dihedral_angle_1_deg 7.104 r_long_range_B_refined 6.713 r_mcangle_it 6.596 r_mcangle_other 6.587 r_long_range_B_other 6.411 r_scangle_other 5.975 r_mcbond_it 5.419 r_rigid_bond_restr 5.412 r_mcbond_other 5.351 r_scbond_it 4.85 r_scbond_other 4.849 r_angle_refined_deg 1.947 r_angle_other_deg 1.712 r_chiral_restr 0.136 r_gen_planes_refined 0.024 r_bond_refined_d 0.019 r_gen_planes_other 0.009 r_bond_other_d 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 564 Nucleic Acid Atoms 1364 Solvent Atoms 265 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing