Experiment: 4JRD

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	RNA WATER SOLUTION PLUS BUFFER (10 MM HEPES, 50 MM NACL, 0.5 MM TCEP, PH 7.0) MIXED 1:1 V/V WITH 2 M (NH4)2SO4 + 0.2 M NH4NO3 AND EQUILIBRATED AGAINST 2 M (NH4)2SO4 + 0.2 M NH4NO3, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
1.49	17.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 22.8	α = 90
b = 22.8	β = 90
c = 163.7	γ = 90

Symmetry
Space Group	P 41 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	100	CCD	MARMOSAIC 300 mm CCD	FOCUSING MIRRORS	2010-05-29	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 210	FOCUSING MIRRORS	2010-10-21	M	SINGLE WAVELENGTH
3	1	x-ray	100	CCD	ADSC QUANTUM 210	FOCUSING MIRRORS	2010-10-21	M	SINGLE WAVELENGTH
4	1	x-ray	100	CCD	ADSC QUANTUM 210	FOCUSING MIRRORS	2010-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1		CLSI	08ID-1
2	SYNCHROTRON	CHESS BEAMLINE A1		CHESS	A1
3	SYNCHROTRON	CHESS BEAMLINE A1		CHESS	A1
4	SYNCHROTRON	CHESS BEAMLINE A1		CHESS	A1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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
1,2,3,4	1	41	92.6	0.0944	34.35	2.73	23042	22972	4	-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2,3,4	1	1.1	73.1		0.1419	4.72	1.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	AB INITIO PHASING	FREE R	1	41	1	23042	22972	1152	92.6	0.126	0.118	0.13	0.158	0.16	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
	242	571

RMS Deviations
Key	Refinement Restraint Deviation
s_approx_iso_adps	0.1
s_from_restr_planes	0.038
s_angle_d	0.021
s_anti_bump_dis_restr	0.021
s_similar_adp_cmpnt	0.015
s_bond_d	0.007
s_rigid_bond_adp_cmpnt	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	478
Solvent Atoms	76
Heterogen Atoms	18

Software

Software
Software Name	Purpose
MxDC	data collection
SHELXD	phasing
SHELXL	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.