2JHP | pdb_00002jhp

The structure of bluetongue virus VP4 reveals a multifunctional RNA- capping production-line

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.7		100 MM IMIDAZOLE PH 8.0, 2%-8% PROPAN-2-OL, 0-250 MM NACL, 50 MM DTT, 2 MM ADOHCY, 5MG/ML VP4 CONCENTRATION, SITTING DROP.

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.242	α = 90
b = 76.242	β = 90
c = 421.508	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 CCD	TORROIDAL MIRRORS	2002-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933, 0.9792	ESRF	ID14-2

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	2.5	30	99.9	0.15	26	24.4		26662		1.2

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	2.5	2.59	99.5		0.54	1.2	12

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.5	20	24542	1244	97.7	0.229	0.226	0.2385	0.289	0.3007	RANDOM	11.49

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]
-0.52	-0.26		-0.52		0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.16
r_scbond_it	21.479
r_scangle_it	20.228
r_dihedral_angle_3_deg	18.826
r_dihedral_angle_4_deg	17.508
r_dihedral_angle_1_deg	13.023
r_mcangle_it	10.915
r_mcbond_it	7.98
r_angle_refined_deg	1.552
r_symmetry_hbond_refined	0.389
r_chiral_restr	0.345
r_nbtor_refined	0.307
r_symmetry_vdw_refined	0.302
r_nbd_refined	0.229
r_xyhbond_nbd_refined	0.17
r_bond_refined_d	0.013
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5040
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	74

Software

Software
Software Name	Purpose
pirate	model building
SCALEPACK	data scaling
SHELXCD	phasing
SHELXD	phasing
SHARP	phasing
pirate	phasing
REFMAC	refinement