6XRQ

Structural descriptions of ligand interactions to DNA and RNA quadruplexes folded from the non-coding region of Pseudorabies virus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6JJH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	283	Potassium cacodylate, Potassium chloride, Sodium cacodylate, MPD

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.177	α = 90
b = 43.974	β = 108.39
c = 30.781	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2019-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96864	Diamond	I24

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.21	27.703	94.1	0.066	0.072	0.028	0.998	11.8	5.7		21248

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.21	1.23	56.5		0.599	0.718	0.387	0.853		3.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6JJH	1.21	27.69	21227	1025	93.879	0.2	0.1999	0.199	0.217	Random Selection	17.82

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]
-0.412		-0.107	1.5		-0.833

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	4.1
r_lrange_other	3.947
r_scangle_it	2.943
r_scangle_other	2.828
r_angle_refined_deg	2.001
r_scbond_it	1.917
r_scbond_other	1.832
r_angle_other_deg	1.82
r_nbtor_refined	0.274
r_nbd_refined	0.237
r_symmetry_nbd_other	0.228
r_nbd_other	0.203
r_symmetry_nbd_refined	0.129
r_chiral_restr	0.12
r_xyhbond_nbd_refined	0.12
r_symmetry_xyhbond_nbd_refined	0.068
r_symmetry_nbtor_other	0.063
r_metal_ion_refined	0.063
r_gen_planes_refined	0.032
r_bond_refined_d	0.025
r_gen_planes_other	0.005
r_bond_other_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	606
Solvent Atoms	97
Heterogen Atoms	119

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction