8CM0

Rhs2-CT endonuclease toxin in complex with cognate immunity protein RhsI2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		previously solved model of Rhs2CT-RhsI2-EF-Tu complex

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		296	Crystals were grown in a condition containing 0.2 uL of 6.5 mg/mL Rhs2CT-RhsI2 (in 20 mM MES & 20 mM imidazole pH 6.0, 150 mM NaCl, 1 mM MgCl2, 0.5 mM TCEP) and 0.2 uL of reservoir solution (0.2 M ammonium acetate, 0.1 M sodium acetate pH 5.0, 20% PEG4K).

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.006	α = 90
b = 81.931	β = 90
c = 101.371	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS3 X 2M		2022-06-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.8731	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.17	37.98	100	0.157	0.07	0.993	8.7	6		17007

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.17	2.24	100		1.511	0.661	0.542

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.17	37.98	16949	842	99.906	0.198	0.195	0.2526	34.743

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]
0.916			-1.073		0.157

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.427
r_dihedral_angle_3_deg	18.868
r_dihedral_angle_4_deg	18.442
r_lrange_it	8.126
r_lrange_other	8.125
r_dihedral_angle_1_deg	6.934
r_scangle_it	6.025
r_scangle_other	6.024
r_mcangle_it	4.349
r_mcangle_other	4.347
r_scbond_it	3.676
r_scbond_other	3.675
r_mcbond_it	2.792
r_mcbond_other	2.79
r_angle_refined_deg	1.477
r_angle_other_deg	1.309
r_nbd_other	0.217
r_nbd_refined	0.206
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.146
r_symmetry_nbd_refined	0.139
r_symmetry_xyhbond_nbd_refined	0.138
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.075
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2185
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
xia2	data scaling
PHASES	phasing