Experiment: 8RMH

Crystal structure of parallel G-quadruplex containing T-tetrads and TG-octaplet

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	A solution containing DNA 1.8 mM, 0.02 M Sodium Cacodylate pH 5.5, 0.1 M NaCl, 0.01 mM MgCl2 was mixed 1:1 with a solution containing 0.2 M Potassium chloride, 0.05 M Sodium cacodylate trihydrate pH 5.9, 10% w/v Polyethylene glycol 4000 & 0.01 M Magnesium chloride hexahydrate.

Crystal Properties
Matthews coefficient	Solvent content
1.89	35.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.436	α = 90
b = 40.436	β = 90
c = 40.479	γ = 90

Symmetry
Space Group	P 4 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293.15	PIXEL	DECTRIS PILATUS 12M		2023-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I23	1.1271	Diamond	I23

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.15	40.48	100	1	0.353	126.9		12480			10.52

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.15	1.17			0.567

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	FREE R-VALUE	1.15	40.48	1.34	12352	1216	98.83	0.1536	0.1514	0.1482	0.19	0.1854	21.33

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
Key	Refinement Restraint Deviation
f_dihedral_angle_d	33.3676
f_angle_d	1.2766
f_chiral_restr	0.0522
f_plane_restr	0.0164
f_bond_d	0.0112

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	290
Solvent Atoms	60
Heterogen Atoms	14

Software

Software
Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
XSCALE	data scaling
ACORN	phasing