5M1O

Crystal structure of the large terminase nuclease from thermophilic phage G20c with bound Cobalt

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M Ammonium Tartrate, 0.1 M Bis-tris pH 5.5-6.5, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.92	36.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.937	α = 90
b = 53.895	β = 91.62
c = 69.751	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	100	PIXEL	DECTRIS PILATUS 6M-F		2016-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9796	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	1.6	42.92	95.7	0.072	0.092	0.057	0.997	6.6	2.1		40243

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	89.5		0.725	0.604		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	SAD	THROUGHOUT	1.6	42.92	38195	2038	95.44	0.1868	0.1849	0.224	RANDOM	22.409

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]
1.99		-0.82	-1.03		-0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.908
r_dihedral_angle_4_deg	14.573
r_dihedral_angle_3_deg	12.037
r_dihedral_angle_1_deg	5.794
r_mcangle_it	1.818
r_angle_refined_deg	1.273
r_mcbond_it	1.083
r_mcbond_other	1.081
r_angle_other_deg	0.883
r_chiral_restr	0.074

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.908
r_dihedral_angle_4_deg	14.573
r_dihedral_angle_3_deg	12.037
r_dihedral_angle_1_deg	5.794
r_mcangle_it	1.818
r_angle_refined_deg	1.273
r_mcbond_it	1.083
r_mcbond_other	1.081
r_angle_other_deg	0.883
r_chiral_restr	0.074
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2914
Nucleic Acid Atoms
Solvent Atoms	322
Heterogen Atoms	2

Software

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