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Transitional unit cell 1 of adenine riboswitch aptamer crystal phase transition upon ligand binding
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TZX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.5 295 40 mM sodium cacodylate, pH 6.5, 80 mM potassium chloride, 100 mM magnesium chloride, 12 mM spermine tetrahydrochloride, 65% v/v (+/-)-2-methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.17 43.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.34 α = 99.29 b = 25.2 β = 90.55 c = 78.74 γ = 90.21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295 PIXEL CS-PAD CXI-1 2017-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.34 SLAC LCLS CXI
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 liquid injection injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 40 (fs) 120 2 9.49 (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 28850 76905 28850
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 GDVN 10 (µl/min) undefined (µm) double-flow focusing 20
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) R Split (All) 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 3 25.17 100 0.9976 0.0734 13.49 751 7656 82.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 100 0.682 1.9061 0.58 207.7
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 4tzx 3.03 25.17 1.96 7285 434 98.61 0.2274 0.2259 0.2286 0.2503 0.2507 91.2944
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 3006 Solvent Atoms Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement SCALA data scaling PDB_EXTRACT data extraction CrystFEL data reduction PHASER phasing