Experiment: 1XJR

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	4.5 mg/ml s2m RNA in 30 mM Tris, pH 7.6, 100 mM NaCl and 60 mM MgCl2 and 50 mM MES, pH 5.6, 100 mM Mg(OAc)-2 and 20% MPD , VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
5.2	73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.218	α = 90
b = 93.218	β = 90
c = 128.109	γ = 120

Symmetry
Space Group	P 65 2 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	ADSC QUANTUM 4		2004-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.98	SSRL	BL9-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.7	80.85	99.4	0.056	0.052	31.3	13.4	9554	9497		-999

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.7	2.85	99.7		0.465	0.434	6.5	13.8	1352

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	THROUGHOUT	2.7	80.85	8516	8516	943	98.97	0.2325	0.2325	0.23136	0.24326	RANDOM	75.177

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]
0.06	0.03		0.06		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	1.924
r_scangle_it	1.757
r_scbond_it	1.075
r_nbtor_refined	0.277
r_nbd_refined	0.169
r_xyhbond_nbd_refined	0.15
r_symmetry_vdw_refined	0.136
r_chiral_restr	0.078
r_metal_ion_refined	0.019
r_bond_refined_d	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	1.924
r_scangle_it	1.757
r_scbond_it	1.075
r_nbtor_refined	0.277
r_nbd_refined	0.169
r_xyhbond_nbd_refined	0.15
r_symmetry_vdw_refined	0.136
r_chiral_restr	0.078
r_metal_ion_refined	0.019
r_bond_refined_d	0.01
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	1024
Solvent Atoms	1
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	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.