8EDP

Crystal structure of a three-tetrad, parallel, and K+ stabilized homopurine G-quadruplex from human chromosome 7


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP298.150.05M MES 6.5, 0.3M potassium chloride, 40% MPD, 0.005M Hexaammine cobalt chloride
Crystal Properties
Matthews coefficientSolvent content
2.2545.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.583α = 90
b = 40.927β = 90
c = 56.018γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray196PIXELDECTRIS EIGER2 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)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
12.0156.0298.20.9868.85.4502762.16
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.012.060.447

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-VALUE4G0F2.0128.011.34497349798.810.24680.24320.278186.87
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_d34.1241
f_angle_d1.4832
f_chiral_restr0.0383
f_plane_restr0.0088
f_bond_d0.0083
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms472
Solvent Atoms5
Heterogen Atoms44

Software

Software
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
Cootmodel building
PHENIXphasing
XDSdata reduction