9R7B | pdb_00009r7b

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		293	0.1M Calcium chloride 20% PEG 6000 10% ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.34	α = 90
b = 61.33	β = 101.95
c = 42.67	γ = 90

Symmetry
Space Group	C 1 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 S 16M		2024-10-02	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	1.09	30.68	79.4	0.036	1	26	11.9		38596

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	1.09	1.11			4.83	0.228

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.1	30.665	38436	1862	81.344	0.169	0.1679	0.1774	0.1852	0.1876	RANDOM	14.89

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]
-1.381		-1.451	-0.111		1.932

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.739
r_lrange_it	11.691
r_lrange_other	10.671
r_dihedral_angle_3_deg	9.887
r_dihedral_angle_2_deg	7.699
r_dihedral_angle_1_deg	6.394
r_scangle_it	5.692
r_scangle_other	5.688
r_mcangle_it	4.57
r_mcangle_other	4.569
r_scbond_it	3.752
r_scbond_other	3.748
r_mcbond_it	2.922
r_mcbond_other	2.904
r_rigid_bond_restr	2.387
r_angle_refined_deg	1.295
r_angle_other_deg	0.473
r_symmetry_nbd_refined	0.209
r_symmetry_nbd_other	0.205
r_nbd_refined	0.197
r_nbd_other	0.193
r_symmetry_xyhbond_nbd_refined	0.176
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.093
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.064
r_gen_planes_refined	0.007
r_bond_refined_d	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	846
Nucleic Acid Atoms
Solvent Atoms	96
Heterogen Atoms

Software

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