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Crystal structure of the Corn aptamer mutant A14U in complex with ThT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BJP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 20 % PEG 4000, 5% PEG 400, 10% glycerol, 0.2 M ammonium acetate pH 6.7, 0.1 M sodium citrate pH 5.6, 0.5 mM ThT
Crystal Properties Matthews coefficient Solvent content 2.84 56.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.723 α = 90 b = 130.723 β = 90 c = 40.674 γ = 120
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 PILATUS3 6M 2018-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.96 37.74 99.9 0.137 0.141 0.032 1 13.8 19 2840 75.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.96 3.04 100 1.062 1.091 0.246 0.516 19.1
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 THROUGHOUT 5BJP 3.101 33.031 1.59 2459 246 99.27 0.2475 0.238 0.2359 0.3298 0.3256 108.9614
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 22.025 f_angle_d 1.688 f_chiral_restr 0.066 f_bond_d 0.008 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 783 Solvent Atoms Heterogen Atoms 41
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction DIALS data reduction