Experiment: 4PCO

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	15 mg/mL RNA, 26.2% (v/v) 2-methyl-2,4-pentanediol (MPD), 0.04 M lithium chloride, 0.03 M cobalt hexamine chloride, 0.04 M sodium cacodylate, pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2	38.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.616	α = 90
b = 43.224	β = 102.48
c = 83.256	γ = 90

Symmetry
Space Group	C 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	CCD	ADSC QUANTUM 315r	Rh coated flat mirrors	2013-06-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.9795, 1.3624, 1.6053, 1.6068	SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (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	1.32	81.289	100	0.06	0.07	0.023	18.2	7.9	29968	29968			11.98

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.32	1.39	100		0.667	0.667	0.289	1.2	7.2	4325

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	FREE R-VALUE	1.32	27.521	0.88	29968	2957	99.92	0.1567	0.1552	0.1835	Random selection

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	7.186
f_angle_d	1.038
f_chiral_restr	0.033
f_plane_restr	0.011
f_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	1060
Solvent Atoms	190
Heterogen Atoms	87

Software

Software
Software Name	Purpose
PHENIX	refinement
SHELX	phasing
SHELX	phasing
PDB_EXTRACT	data extraction
Coot	model building
Blu-Ice	data collection
SCALA	data scaling
SHELXD	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.