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Structure of Centromeric Satellite III Non-canonical Duplex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 175D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 Tris-Acetate, potassium acetate, magnesium acetate, MES monohydrate, 2-Methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.19 48.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.522 α = 90 b = 40.217 β = 90 c = 55.379 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 196 PIXEL DECTRIS EIGER X 16M 2019-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 1.07110 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.57 32.54 99.7 0.998 15.1 5.9 12855 31.32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.57 1.63 99 0.991 2.5 5.1
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 175D 1.57 32.54 1.35 12659 1257 98.45 0.224 0.2206 0.2279 0.2551 0.2625 48.43
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 33.668 f_angle_d 1.668 f_chiral_restr 0.1189 f_bond_d 0.017 f_plane_restr 0.0166
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 636 Solvent Atoms 74 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement XDS data scaling pointless data scaling Aimless data scaling PHASER phasing Coot model building XDS data reduction