5OEA

Structure of large terminase from the thermophilic bacteriophage D6E in complex with ATP-gamma-S (Crystal form 3)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1.2 M Ammonium Sulafte, 0.1 M HEPES pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.476	α = 90.98
b = 102.981	β = 119.37
c = 103.044	γ = 117.18

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	PIXEL	DECTRIS PILATUS 6M-F		2016-07-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9795	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	3	45.9	96.5	0.075	0.104	0.071	0.996	6.3	1.9		59382

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.08	96.5		0.811	1.123	0.775	0.379		2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3	45.9	56215	3165	96.43	0.1928	0.1895	0.2533	RANDOM	79.046

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]
-2.04	0.13	-1.06	4	0.13	-1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.6
r_dihedral_angle_3_deg	14.036
r_dihedral_angle_4_deg	11.723
r_dihedral_angle_1_deg	6.366
r_angle_refined_deg	1.111
r_angle_other_deg	0.864
r_chiral_restr	0.064
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.6
r_dihedral_angle_3_deg	14.036
r_dihedral_angle_4_deg	11.723
r_dihedral_angle_1_deg	6.366
r_angle_refined_deg	1.111
r_angle_other_deg	0.864
r_chiral_restr	0.064
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19345
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	110

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.