Experiment: 3MJ3

Cricket Paralysis Virus IGR IRES Domain 3 RNA bound to selenate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3B31	PDB entry 3B31

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	293	1.4 M lithium sulfate, 42.5 mM Magnesium chloride, 0.5 mM spermidine, 10 mM HEPES-KOH, 50 mM HEPES-NaOH; transferred to saturated lithium selenate, 42.5 mM Magnesium chloride, 0.5 mM spermidine, 10 mM HEPES-KOH, 50 mM HEPES-NaOH for cryo-protection, pH 7.5, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.19	61.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.26	α = 90
b = 59.26	β = 90
c = 99.775	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						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.9756	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.1	50	99.4				3580	2	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (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	PDB entry 3B31	3.1	30	3580	644	96.2	0.227	0.2339	0.263	0.2717	RANDOM 10%	48.699

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]
-11.813			7.274		4.538

RMS Deviations
Key	Refinement Restraint Deviation
c_mcangle_it	2.513
c_mcbond_it	1.53
c_angle_d	1.395
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	917
Solvent Atoms
Heterogen Atoms	20

Software

Software
Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction