7YHL | pdb_00007yhl

Crystal Structure of the ring nuclease Sso2081 from Saccharolobus solfataricus in complex with free phosphate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		298	0.1 M Sodium acetate trihydrate, pH 4.5, 25% w/v Polyethylene glycol 1500

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.027	α = 90
b = 38.376	β = 106.412
c = 69.798	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		2022-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.97919	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	2.7	40.95	95.55	0.067	0.998	10.9	5.29		9099

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	2.7	2.79	95.55		0.748	0.805	1.5	5.32

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	SAD	THROUGHOUT	2.7	40.95	9098	483	93.862	0.264	0.2631	0.27	0.2877	0.29	117.165

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]
2.966		2.857	-2.26		-2.036

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	28.921
r_lrange_other	28.921
r_scangle_other	19.069
r_scangle_it	19.041
r_mcangle_it	18.559
r_mcangle_other	18.553
r_dihedral_angle_3_deg	16.973
r_dihedral_angle_6_deg	15.479
r_mcbond_it	12.983
r_mcbond_other	12.98
r_scbond_it	12.966
r_scbond_other	12.931
r_dihedral_angle_1_deg	9.505
r_dihedral_angle_2_deg	7.48
r_angle_refined_deg	1.802
r_angle_other_deg	0.633
r_nbd_other	0.257
r_symmetry_nbd_other	0.218
r_xyhbond_nbd_refined	0.191
r_nbd_refined	0.188
r_nbtor_refined	0.188
r_symmetry_nbd_refined	0.16
r_symmetry_nbtor_other	0.09
r_chiral_restr	0.071
r_symmetry_xyhbond_nbd_other	0.029
r_bond_other_d	0.018
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_ext_dist_refined_b

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2697
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data scaling
MOLREP	phasing
PHENIX	model building
Coot	model building
XDS	data reduction