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Crystal structure of the major quadruplex formed in the human c-MYC promoter
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WO2 4WO2, 1XAV experimental model PDB 1XAV 4WO2, 1XAV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277.15 20% MPD
300mM KCl
50mM LiCl
50mM Sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.76 55.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.663 α = 90 b = 69.811 β = 90 c = 32.952 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 PILATUS 6M 2017-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.979 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.35 35.03 99.4 0.013 1 34 12.6 6774 55.55
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.43 99.7 0.167 0.966 4.4 12.9 652
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4WO2, 1XAV 2.35 34.906 1.36 6624 671 98.57 0.2229 0.2203 0.2241 0.2455 0.248 80.2
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 35.1 f_angle_d 1.08 f_chiral_restr 0.05 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 934 Solvent Atoms 16 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement REFMAC refinement XDS data reduction XDS data scaling PHASER phasing