9T38 | pdb_00009t38

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EFC
experimental model	Other		Solved and refined by X-ray crystallography in this study (not previously deposited)
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		296	0.2 uL of 18 mg/mL Rhs2-ct-RhsI2-EF-Tu (in 20 mM Tris-HCl pH 7.5, 250 mM NaCl, 2 mM MgCl2, 2 mM GDP and 0.5 mM TCEP) mixed with 0.2 uL of reservoir solution (0.2 M ammonium actetate, 0.1 M HEPES pH 7.5 and 25% PEG3350). Cryoprotected with Paratone N

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.598	α = 90
b = 110.569	β = 102.392
c = 113.863	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 EIGER2 XE 16M		2021-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.45	60.236	100	0.151	0.988	6	6.7		54856

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	2.45	2.52			1.721	1.134	0.443

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.45	60.236	54781	2724	99.896	0.273	0.2704	0.2736	0.3138	0.3163	57.338

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]
-3.327		0.085	-0.509		3.464

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.676
r_dihedral_angle_4_deg	20.108
r_dihedral_angle_3_deg	15.661
r_lrange_it	9.916
r_lrange_other	9.916
r_dihedral_angle_1_deg	6.273
r_mcangle_it	5.5
r_mcangle_other	5.499
r_scangle_it	5.464
r_scangle_other	5.464
r_mcbond_it	3.595
r_mcbond_other	3.594
r_scbond_it	3.455
r_scbond_other	3.455
r_angle_other_deg	1.381
r_angle_refined_deg	1.265
r_nbd_other	0.255
r_symmetry_nbd_refined	0.223
r_symmetry_nbd_other	0.201
r_nbd_refined	0.187
r_xyhbond_nbd_refined	0.165
r_nbtor_refined	0.16
r_metal_ion_refined	0.141
r_ncsr_local_group_2	0.086
r_ncsr_local_group_3	0.083
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_refined	0.074
r_ncsr_local_group_1	0.069
r_chiral_restr	0.057
r_symmetry_xyhbond_nbd_other	0.011
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10265
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	76

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing