9SMA | pdb_00009sma

Structure and mechanism of the broad spectrum CRISPR-associated ring nuclease Crn4

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	4.5	293	0.1 M Sodium acetate pH 4.5 22 % v/v PEG Smear Broad

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.314	α = 90
b = 116.314	β = 90
c = 38.863	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 XE 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	2.34	100.8	90.6	0.182	0.996	10.4	8		12327

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.34	2.38			0.375

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	2.34	100.731	12289	604	94.633	0.225	0.2221	0.227	0.2824	0.2851	40.675

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]
0.04	0.02		0.04		-0.131

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	12.355
r_dihedral_angle_3_deg	10.979
r_dihedral_angle_2_deg	8.211
r_dihedral_angle_1_deg	7.001
r_lrange_it	6.245
r_lrange_other	6.243
r_mcangle_it	3.61
r_mcangle_other	3.609
r_scangle_it	3.591
r_scangle_other	3.589
r_mcbond_it	2.089
r_mcbond_other	2.086
r_scbond_it	2.063
r_scbond_other	2.061
r_angle_refined_deg	1.075
r_angle_other_deg	0.395
r_symmetry_nbd_refined	0.209
r_nbd_refined	0.208
r_symmetry_nbd_other	0.206
r_nbtor_refined	0.162
r_nbd_other	0.148
r_xyhbond_nbd_refined	0.146
r_ncsr_local_group_1	0.131
r_symmetry_xyhbond_nbd_refined	0.089
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.047
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1897
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms

Software

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