5E54

Two apo structures of the adenine riboswitch aptamer domain determined using an X-ray free electron laser


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.529540 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 coefficientSolvent content
2.2745.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.91α = 90
b = 46.72β = 94.06
c = 92.25γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295PIXELCS-PAD CXI-12015-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE CXI1.3SLAC LCLSCXI

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Split (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.325.021000.10924.37461.31860270.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.381000.81510.27314.61823

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.325.0216995100397.90.21560.21310.2562RANDOM77.187
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]
-0.96-0.282.17-1.16
RMS Deviations
KeyRefinement Restraint Deviation
r_scbond_it3.921
r_angle_refined_deg1.619
r_chiral_restr0.106
r_gen_planes_refined0.014
r_bond_refined_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms2826
Solvent Atoms14
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building
Cheetahdata collection
CrystFELdata reduction
CrystFELdata scaling