9R8S | pdb_00009r8s

A viral SAVED protein with ring nuclease activity subverts type III CRISPR defence

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	10.5	293	1.2M sodium phosphate 0.8M potassium phosphate 0.2M lithium phosphate 0.1M CAPS pH 10.5

Crystal Properties
Matthews coefficient	Solvent content
3.71	66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.614	α = 90
b = 110.614	β = 90
c = 113.027	γ = 120

Symmetry
Space Group	P 31 2 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 X 16M		2024-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

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	1.79	95.93	100	0.115	1	17.4	38.9		75593

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	1.79	1.82	100		4.572	0.345

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	AB INITIO PHASING	THROUGHOUT	1.79	95.794	75149	1997	99.467	0.166	0.1649	0.1783	0.2071	0.2167	RANDOM	41.399

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]
-0.769	-0.384		-0.769		2.493

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	27.873
r_lrange_other	27.827
r_scangle_it	24.653
r_scangle_other	24.607
r_mcangle_other	19.333
r_mcangle_it	19.328
r_scbond_it	18.196
r_scbond_other	18.151
r_mcbond_it	14.596
r_mcbond_other	14.587
r_dihedral_angle_6_deg	14.12
r_dihedral_angle_3_deg	11.106
r_dihedral_angle_1_deg	7.179
r_dihedral_angle_2_deg	5.064
r_rigid_bond_restr	3.307
r_angle_refined_deg	1.314
r_angle_other_deg	0.444
r_nbd_refined	0.215
r_symmetry_nbd_other	0.198
r_symmetry_xyhbond_nbd_refined	0.198
r_nbtor_refined	0.185
r_nbd_other	0.181
r_ncsr_local_group_1	0.148
r_xyhbond_nbd_refined	0.128
r_xyhbond_nbd_other	0.116
r_symmetry_nbd_refined	0.095
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.066
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3811
Nucleic Acid Atoms
Solvent Atoms	204
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing