8EBO

Homopurine parallel G-quadruplex from human chromosome 7 stabilized by K+ ions


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4G0F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP285.15The well condition included 0.012 M NaCl, 0.08-0.1 M KCl, 0.04 M sodium cacodylate pH 5.5, 45% MPD, and 0.002 M hexammine cobalt(III) chloride
Crystal Properties
Matthews coefficientSolvent content
2.1843.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.053α = 90
b = 47.474β = 90
c = 119.597γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray196PIXELDECTRIS EIGER X 16M2021-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97918APS24-ID-C

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9830.4499.20.0490.0540.0230.99915.15.8429664.73
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)
11.982.0399.80.8940.3510.76.3

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4G0F1.9824.711.35425442598.090.23620.23140.278995.26
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_d36.279
f_angle_d1.9337
f_chiral_restr0.0686
f_bond_d0.0142
f_plane_restr0.0128
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms435
Solvent Atoms4
Heterogen Atoms37

Software

Software
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
Cootmodel building
PHENIXphasing
XDSdata reduction