6JJH | pdb_00006jjh

Crystal structure of a two-quartet RNA parallel G-quadruplex complexed with the porphyrin TMPyP4

X-RAY DIFFRACTION

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
2.29	46.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.856	α = 90
b = 23.647	β = 107.59
c = 31.052	γ = 90

Symmetry
Space Group	P 1 2 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 PILATUS 12M		2018-06-27	M	SINGLE WAVELENGTH
2	1	x-ray	100	PIXEL	DECTRIS PILATUS 12M		2018-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I23	1.7712	Diamond	I23
2	SYNCHROTRON	DIAMOND BEAMLINE I23	3.3509	Diamond	I23

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.74	29.6	99.5	0.021	1	15.6	6.24		4377

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.74	1.8	98.6		0.34	0.842	1.76

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.74	29.6	4142	236	99.7	0.2418	0.2393	0.24	0.2914	0.3	RANDOM	42.481

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]
-1.47		0.38	-1.47		2.24

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	1.403
r_angle_other_deg	1.379
r_chiral_restr	0.105
r_gen_planes_refined	0.012
r_bond_refined_d	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	303
Solvent Atoms	11
Heterogen Atoms	107

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
Aimless	data scaling
HKL2Map	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.