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Crystal structure of AUGUGGCAU duplex with cesium ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8AMG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 292 0.08 M NaCl
0.02 M CsCl
0.04 M cacodylate sodium
45% MPD
0.012 M spermine
Crystal Properties Matthews coefficient Solvent content 2.22 44.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.231 α = 90 b = 90.612 β = 91.427 c = 139.933 γ = 90
Symmetry Space Group P 1 21 1
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 2017-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.917143 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.86 45.31 96 0.08 0.999 8.51 3.5 30808 87.12
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.86 3.03 1.586 0.527 0.81
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 8AMG 2.86 45.31 1.92 30638 1828 95.53 0.2238 0.221 0.2151 0.2688 0.2662 93.02
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 10.4533 f_angle_d 0.4645 f_chiral_restr 0.0196 f_plane_restr 0.0019 f_bond_d 0.0016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 5320 Solvent Atoms Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing