4KFU | pdb_00004kfu

Structure of the genome packaging NTPase B204 from Sulfolobus turreted icosahedral virus 2 in complex with AMPPCP

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	295	0.1 M Tris-HCl, 0.2 M magnesium chloride, 30% PEG8000, 5 mM AMPPCP, protein in 50 mM sodium citrate, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.558	α = 90.85
b = 65.227	β = 93.77
c = 72.118	γ = 91.56

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	MARMOSAIC 225 mm CCD		2011-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87260	ESRF	ID23-2

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	1.89	48.717	97.4	0.085	11.78	3.94	65868	65868			32.05

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	1.89	2.01	92.4		0.708	1.94	3.9	10093

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	PDB ENTRY 4KFR	1.892	48.717	1.99	65852	65852	3296	97.41	0.1906	0.1883	0.19	0.2336	0.23	RANDOM

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]
-3.6749	0.0473	2.8092	8.9918	-1.2774	-5.3169

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.504
f_angle_d	1.14
f_chiral_restr	0.078
f_bond_d	0.011
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6352
Nucleic Acid Atoms
Solvent Atoms	428
Heterogen Atoms	214

Software

Software
Software Name	Purpose
MxCuBE	data collection
SHARP	phasing
PHENIX	refinement
XDS	data reduction
XDS	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.