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Crystal Structure of a DNA G-Quadruplex with a Cytosine Bulge
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XAV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 2.5 M NaCl, 10% v/v ethanol, 0.1 M sodium cacodylate, G4R1 53-105 peptide (UniProtKB Q9H2U1/DHX36_HUMAN, amino acid residues 53-105)
Crystal Properties Matthews coefficient Solvent content 2.33 47.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.103 α = 64.65 b = 33.1 β = 78.64 c = 33.282 γ = 81.78
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ Rigaku Osmic Confocal Max-Flux multilayer mirror 2015-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54187
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 1.7963 20.3024 96 0.072 9 3.8 9658 -3 33.5
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 1.7963 1.91 66.23 0.806 1.5 3.5
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 1XAV 1.8802 19.4935 8254 603 95.99 0.2288 0.2274 0.2325 0.2474 0.2521 RANDOM 39.929
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] -0.4 0.76 -0.85 0.93 -0.28 -0.57
RMS Deviations Key Refinement Restraint Deviation r_angle_other_deg 2.461 r_angle_refined_deg 1.067 r_chiral_restr 0.069 r_gen_planes_refined 0.011 r_gen_planes_other 0.009 r_bond_refined_d 0.004 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 838 Solvent Atoms 78 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction PHASER phasing