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A bimolecular anti-parallel-stranded Oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine BSU-6042 in a large unit cell
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L1H PDB entry 1L1H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 285.15 2 microliter drops containing 5% v/v MPD, 0.50 mM DNA, 0.25 mM Ligand, 40 mM Potassium chloride, 5 mM Magnesium chloride, 4.1 Spermine equilibrated against 35% v/v MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285.15K
Crystal Properties Matthews coefficient Solvent content 1.88 34.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.356 α = 90 b = 42.542 β = 90 c = 48.636 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 IMAGE PLATE RIGAKU RAXIS IV mirrors 2006-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.2 27.72 94.5 0.087 8.3 3.61 6193 5854 3 34.254
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) 2.2 2.28 92.1 0.181 5.2 3.59 545
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB entry 1L1H 2.2 27.68 5854 5575 277 94.51 0.23691 0.23422 0.2288 0.28506 0.2796 RANDOM 20.772
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] -0.36 -3.27 3.63
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.219 r_angle_refined_deg 2.15 r_scbond_it 1.817 r_nbd_refined 0.34 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.224 r_symmetry_hbond_refined 0.21 r_xyhbond_nbd_refined 0.204 r_metal_ion_refined 0.14 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.219 r_angle_refined_deg 2.15 r_scbond_it 1.817 r_nbd_refined 0.34 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.224 r_symmetry_hbond_refined 0.21 r_xyhbond_nbd_refined 0.204 r_metal_ion_refined 0.14 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1012 Solvent Atoms 162 Heterogen Atoms 102
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling