7YGH | pdb_00007ygh

Crystal Structure of the ring nuclease Sso2081 from Saccharolobus solfataricus in complex with cyclic-tetraadenylate (cA4)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7YHL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		298	0.1 M Sodium acetate trihydrate, pH 5.0, 22% w/v Polyethylene glycol monomethyl ether 550, 5% w/v n-Dodecyl-B-D-maltoside

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.052	α = 90
b = 38.837	β = 105.798
c = 72.965	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 S 9M		2022-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.97918	SSRF	BL02U1

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	3.11	50	99.57	0.07	0.997	22.84	3.7		6715

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	3.11	3.22	100		0.786	0.602	1.88

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	7YHL	3.11	28.556	6710	328	99.54	0.239	0.2379	0.24	0.2584	0.25	RANDOM	136.267

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]
-1.611		3.216	-0.998		0.681

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	38.41
r_lrange_other	38.409
r_mcangle_it	30.398
r_mcangle_other	30.391
r_scangle_it	29.122
r_scangle_other	29.116
r_mcbond_it	21.768
r_mcbond_other	21.768
r_scbond_it	19.825
r_scbond_other	19.821
r_dihedral_angle_6_deg	16.526
r_dihedral_angle_3_deg	16.191
r_dihedral_angle_1_deg	9.048
r_dihedral_angle_2_deg	5.948
r_angle_refined_deg	1.71
r_angle_other_deg	0.65
r_symmetry_xyhbond_nbd_refined	0.284
r_nbd_other	0.231
r_symmetry_nbd_refined	0.22
r_symmetry_nbd_other	0.209
r_nbtor_refined	0.175
r_nbd_refined	0.169
r_xyhbond_nbd_refined	0.164
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.083
r_symmetry_xyhbond_nbd_other	0.021
r_bond_refined_d	0.01
r_bond_other_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2850
Nucleic Acid Atoms	88
Solvent Atoms	1
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
MOLREP	phasing
Coot	model building
PHENIX	model building
HKL-2000	data reduction