3B31 | pdb_00003b31

Crystal structure of domain III of the Cricket Paralysis Virus IRES RNA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	303	1.4 M lithium sulfate, 40 mM magnesium acetate, 50 mM HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.724	α = 90
b = 58.724	β = 90
c = 98.989	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		IMAGE PLATE	RIGAKU RAXIS IV++			M	SINGLE WAVELENGTH
2	1	x-ray		CCD	ADSC QUANTUM 315			M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418
2	SYNCHROTRON	ALS BEAMLINE 12.3.1	1.1055, 1.1053	ALS	12.3.1

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	2.4	23.2	99.7	0.09	0.09	27.2	31.9	7247	7225	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.4	2.49	99.7		2	18.3	696

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MAD	2.4	23.2	2	2	7247	7225	774	99.7	0.2393	0.2292	0.2686	0.258

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]
-2.917			-2.917		5.834

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_deg	1.35
c_bond_d	0.0053

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	913
Solvent Atoms	146
Heterogen Atoms	25

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
CNS	refinement
ELVES	data reduction
MOSFLM	data reduction
CCP4	data scaling
PHENIX	phasing