5EW7

Crystal structure of C9ORF72 Antisense CCCCGG repeat RNA associated with Lou Gehrig's disease and frontotemporal dementia, crystallized with Ba2+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5EW4PDB entry 5EW4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62930.04 M sodium cacodylate, 50 mM KCl, 0.08 M NaCl, 0.012 M spermine, 0.02 M barium chloride, 10% (v/v) (+/-)-2-methyl-2,4-pentanediol, equilibrated against 35% (v/v) (+/-)-2-methyl-2,4-pentanediol
Crystal Properties
Matthews coefficientSolvent content
2.1141.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.134α = 90
b = 47.659β = 90
c = 59.495γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmonochromator2014-08-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.91967APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (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
11.755099.90.0490.0530.0239.75.81228119.56
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.781000.5060.765.3588

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUEPDB entry 5EW41.7537.1961.3411264112691.740.23690.23460.2575random27.1189
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d5.178
f_angle_d0.419
f_chiral_restr0.022
f_bond_d0.017
f_plane_restr0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms818
Solvent Atoms100
Heterogen Atoms9

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing