3FHD | pdb_00003fhd

Crystal structure of the Shutoff and Exonuclease Protein from Kaposis Sarcoma Associated Herpesvirus

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	0.2M Lithium sulfate, 0.1M Bis-TRIS, 25%PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.247	α = 95.48
b = 48.905	β = 106.86
c = 67.294	γ = 104.27

Symmetry
Space Group	P 1

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	MAR CCD 165 mm		2007-06-07	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 4		2007-06-28	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.97954	BESSY	14.2
2	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.93300	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	1.85	46.63		0.073	12.1	3.4		41764			28.119

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	SAD	THROUGHOUT	1.85	46.63	39306	2096	96.37	0.18582	0.18356	0.1832	0.22807	0.2296	RANDOM	23.126

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]
0.41	0.44	0.29	0.3	0.27	-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.498
r_dihedral_angle_4_deg	19.42
r_dihedral_angle_3_deg	13.496
r_dihedral_angle_1_deg	5.72
r_scangle_it	3.308
r_scbond_it	2.27
r_mcangle_it	1.482
r_angle_refined_deg	1.35
r_mcbond_it	0.876
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.498
r_dihedral_angle_4_deg	19.42
r_dihedral_angle_3_deg	13.496
r_dihedral_angle_1_deg	5.72
r_scangle_it	3.308
r_scbond_it	2.27
r_mcangle_it	1.482
r_angle_refined_deg	1.35
r_mcbond_it	0.876
r_nbtor_refined	0.304
r_nbd_refined	0.199
r_symmetry_hbond_refined	0.191
r_symmetry_vdw_refined	0.181
r_xyhbond_nbd_refined	0.139
r_chiral_restr	0.096
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3591
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	16

Software

Software
Software Name	Purpose
SOLVE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.