7Z55 | pdb_00007z55

Crystal Structure of the Ring Nuclease 0455 from Sulfolobus islandicus (Sis0455) in complex with its substrate

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	41% PEG 400 0.1M sodium acetate pH 4.5 0.1M Li2SO4

Crystal Properties
Matthews coefficient	Solvent content
1.78	30.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.975	α = 90
b = 79.531	β = 90
c = 95.74	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER X 16M		2021-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.979	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.54	61.24	84.2	0.999	18	24.4		37215

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	1.54	1.65			0.488

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	FREE R-VALUE	1.664	47.916	36894	1938	98.859	0.211	0.2086	0.21	0.2518	0.25	37.293

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]
-0.052			0.222		-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.105
r_dihedral_angle_4_deg	18.113
r_dihedral_angle_3_deg	15.53
r_dihedral_angle_1_deg	7.385
r_lrange_other	7.338
r_lrange_it	7.337
r_scangle_it	5.775
r_scangle_other	5.774
r_mcangle_it	4.377
r_mcangle_other	4.377
r_scbond_it	3.987
r_scbond_other	3.986
r_mcbond_it	3.179
r_mcbond_other	3.155
r_angle_refined_deg	2.042
r_angle_other_deg	1.448
r_nbd_other	0.29
r_symmetry_nbd_refined	0.253
r_nbd_refined	0.224
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.148
r_symmetry_xyhbond_nbd_refined	0.132
r_chiral_restr	0.098
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2999
Nucleic Acid Atoms	88
Solvent Atoms	36
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
CRANK2	phasing