7YGL | pdb_00007ygl

Crystal Structure of the ring nuclease Sso2081 from Saccharolobus solfataricus in complex with A4>p cleavage intermediate

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, 20% w/v Polyethylene glycol 1500

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.51	α = 90
b = 39.144	β = 105.178
c = 74.088	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	80	PIXEL	DECTRIS PILATUS3 6M		2019-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.978	SSRF	BL19U1

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	2.5	50	99.9	0.043	0.997	32.22	6.4		13097

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	2.5	2.59	98		0.851	0.897	1.86	5.8

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	2.5	28.91	13090	683	98.785	0.259	0.2578	0.26	0.2786	0.27	RANDOM	114.148

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]
-3.444		0.787	7.902		-4.259

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	30.288
r_lrange_other	30.287
r_scangle_it	25.293
r_scangle_other	25.287
r_mcangle_it	24.183
r_mcangle_other	24.177
r_mcbond_it	18.545
r_mcbond_other	18.544
r_scbond_it	18.532
r_scbond_other	18.53
r_dihedral_angle_6_deg	16.47
r_dihedral_angle_3_deg	15.693
r_dihedral_angle_1_deg	8.437
r_dihedral_angle_2_deg	5.953
r_angle_refined_deg	1.759
r_angle_other_deg	0.626
r_symmetry_xyhbond_nbd_refined	0.259
r_nbd_other	0.234
r_symmetry_nbd_other	0.207
r_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.175
r_nbd_refined	0.155
r_symmetry_nbd_refined	0.103
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.082
r_symmetry_xyhbond_nbd_other	0.013
r_bond_refined_d	0.01
r_bond_other_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2856
Nucleic Acid Atoms	88
Solvent Atoms	6
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