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Monomeric antiparallel G-quadruplex formed by d(G4C2)4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2N2D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 0.05 M KCl, 0.05 M BIS-TRIS at pH 7.0, 33% w/v PEG 3350 and 0.005 M spermine
Crystal Properties Matthews coefficient Solvent content 2.22 44.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.288 α = 90 b = 87.147 β = 90 c = 98.302 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 100 PIXEL DECTRIS EIGER2 S 9M 2024-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.919764 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.7 50 99.8 0.16 0.169 1 12.12 9.8 7881
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.86 99.2 1.577 1.676 0.335 1.74 8.88
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 2N2D 2.7 43.61 7100 775 99.7 0.23518 0.23336 0.2313 0.2516 0.2481 RANDOM 66.503
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] -1.35 2.15 -0.8
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 7.791 r_long_range_B_other 7.786 r_scangle_other 3.063 r_scbond_it 1.924 r_scbond_other 1.924 r_angle_refined_deg 1.894 r_angle_other_deg 0.538 r_chiral_restr 0.066 r_gen_planes_refined 0.012 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 7.791 r_long_range_B_other 7.786 r_scangle_other 3.063 r_scbond_it 1.924 r_scbond_other 1.924 r_angle_refined_deg 1.894 r_angle_other_deg 0.538 r_chiral_restr 0.066 r_gen_planes_refined 0.012 r_bond_refined_d 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1894 Solvent Atoms 6 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction