5JBG | pdb_00005jbg

Crystal structure of chicken LGP2 with 5'ppp 26-mer hairpin RNA with 3' GG overhang and ADP-AlF4-Mg2+ at 2.0 A resolution.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5JB2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	277	chLGP2, directly after size exclusion chromatography, was mixed with dsRNA in a 1:1 ratio and incubated for 30 minutes on ice. The complex was concentrated with an Amicon Ultra concentrator to around 10 mg/ml and then 2 mM ADP:AlF4 and 2 mM MgCl2 were added. 5 prime triphosphate, 3 prime GG overhang 26-mer hairpin RNA:ADP:AlF4 complex was mixed with reservoir buffer containing 0.1 M citric acid pH 5.0, 0.8 M ammonium sulphate in a 1:1 ratio.

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.86	α = 90
b = 97.43	β = 90
c = 122.58	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2015-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.072	ESRF	ID29

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	76.27	99.9	0.259	6.31	4.47		56661

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	2.1	98.7		0.795	1.38	4.35

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	5JB2	2	76.27	53847	2814	98.95	0.21945	0.21758	0.22	0.255	0.26	RANDOM	38.664

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]
2.5			-0.76		-1.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.751
r_dihedral_angle_4_deg	16.982
r_dihedral_angle_3_deg	14.289
r_long_range_B_refined	6.437
r_long_range_B_other	6.181
r_dihedral_angle_1_deg	5.845
r_scangle_other	3.527
r_mcangle_it	3.286
r_mcangle_other	3.286
r_scbond_it	2.1
r_scbond_other	2.091
r_mcbond_it	1.995
r_mcbond_other	1.989
r_angle_refined_deg	1.278
r_angle_other_deg	0.93
r_chiral_restr	0.07
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5290
Nucleic Acid Atoms	506
Solvent Atoms	268
Heterogen Atoms	59

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing