Experiment: 7UCR

Joint X-ray/neutron structure of the Sarcin-Ricin loop RNA

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DVZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291.15	0.233 mM RNA, 1.0 M ammonium sulfate, 2 mM magnesium chloride, 2 mM manganese chloride, 16.5 mM -3-(N-morpholino)propanesulfonic acid.

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.495	α = 90
b = 29.495	β = 90
c = 76.52	γ = 90

Symmetry
Space Group	P 43

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	Bruker PHOTON III		2020-02-14	M	SINGLE WAVELENGTH
2	1	neutron	100	AREA DETECTOR	ORNL ANGER CAMERA		2020-01-29	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	Excillum MetalJet D2 70 kV	1.342
2	SPALLATION SOURCE	ORNL Spallation Neutron Source BEAMLINE MANDI	2.0-4.0	ORNL Spallation Neutron Source	MANDI

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	0.998	16.05	99.67	0.055				0.999		21.66	13.68		35326			8.3
2	2.25	12.34	92.32	0.212				0.886		9.8	3.4		2887			8.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.998	1.033		0.412				0.849
2	2.25	2.33		0.299				0.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MOLECULAR REPLACEMENT	1	16.05		1.34		35272	3483	99.42		0.1812	0.1785	0.1799	0.1965	0.1986		17.21
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2.25	12.34				2886		92.32			0.2543		0.2987

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	23.333
f_angle_d	1.6111
f_chiral_restr	0.1076
f_plane_restr	0.0129
f_bond_d	0.0115

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	579
Solvent Atoms	80
Heterogen Atoms	5

Software

Software
Software Name	Purpose
PHENIX	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
PHENIX	phasing