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Racemic crystal structure of a bimolecular DNA G-quadruplex (P-1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HBN PDB ENTRY 2HBN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 285 1 mM DNA, 50 mM potassium cacodylate, 40 mM potassium chloride, 50 mM magnesium chloride hexahydrate, 2.5 mM spermine, 5% v/v MPD, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.05 39.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.646 α = 104.5 b = 28.3 β = 94.19 c = 45.719 γ = 113.42
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 200K 2013-12-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 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 1.9 25.02 94.89 0.0628 7.81 1.7 9497 9011 2 2 49.29
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 1.9 1.97 95.66 0.1227 2.66 1.5 909
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 2HBN 1.9 25.02 9075 8599 412 94.75 0.28797 0.28562 0.2902 0.34003 0.3509 RANDOM 14.068
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] -0.06 -0.02 0.06 0.03 0.01
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 4.991 r_long_range_B_other 4.348 r_angle_other_deg 1.652 r_angle_refined_deg 1.049 r_scangle_other 1.02 r_scbond_it 0.619 r_scbond_other 0.619 r_chiral_restr 0.075 r_gen_planes_refined 0.014 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 4.991 r_long_range_B_other 4.348 r_angle_other_deg 1.652 r_angle_refined_deg 1.049 r_scangle_other 1.02 r_scbond_it 0.619 r_scbond_other 0.619 r_chiral_restr 0.075 r_gen_planes_refined 0.014 r_bond_refined_d 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 506 Solvent Atoms 143 Heterogen Atoms 5
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling