4JNG | pdb_00004jng

Schmallenberg virus nucleoprotein-RNA complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4IDX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.7	298	0.1M Bis-Tris pH5.7, 0.3M NaCl, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.35	α = 90
b = 85.96	β = 102.02
c = 77.33	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	173	CCD	ADSC QUANTUM 315r	mirrors	2013-01-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.92	Diamond	I04

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	2.12	37.82	97.9	0.061	0.07	2	4.1	54454	54303	2.6	2.6	32

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)
1	2.16	37.81	99.2		0.572	0.65	2.6	4.3	7984

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	4IDX	2.12	37.4	2	54303	51526	2755	97.7	0.266	0.26548	0.26449	0.2805	0.28348	0.3018	RANDOM	19.666

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]
-2.87		0.56	-2.79		5.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.468
r_sphericity_free	31.054
r_dihedral_angle_3_deg	19.41
r_dihedral_angle_4_deg	16.765
r_dihedral_angle_1_deg	7.318
r_sphericity_bonded	3.41
r_rigid_bond_restr	2.654
r_angle_refined_deg	1.303
r_angle_other_deg	0.914
r_chiral_restr	0.08
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7035
Nucleic Acid Atoms	840
Solvent Atoms	163
Heterogen Atoms

Software

Software
Software Name	Purpose
iMOSFLM	data reduction
PHASER	phasing
REFMAC	refinement
SCALA	data scaling