7Z56

Crystal Structure of the Ring Nuclease 0455 from Sulfolobus islandicus (Sis0455) in its apo form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7Z55

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	22% PEG 4000 0.05 M Tricine pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
1.83	32.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.423	α = 90
b = 51	β = 98.696
c = 80.353	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 EIGER X 16M		2020-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	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	1.91	79.43	85.2	0.995	9.7	6.3		19381

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	1.91	2.05			0.191

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7Z55	2.27	79.429	15733	776	98.801	0.185	0.1815	0.2534	54.421

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]
0.316		-0.287	-0.496		0.256

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.738
r_dihedral_angle_4_deg	22.807
r_dihedral_angle_3_deg	20.646
r_lrange_it	8.955
r_lrange_other	8.953
r_dihedral_angle_1_deg	7.328
r_scangle_it	6.796
r_scangle_other	6.794
r_mcangle_it	4.63
r_mcangle_other	4.629
r_scbond_it	4.11
r_scbond_other	4.109
r_mcbond_it	3.157
r_mcbond_other	3.146
r_angle_refined_deg	1.829
r_angle_other_deg	1.373
r_nbd_refined	0.218
r_nbd_other	0.202
r_symmetry_nbd_other	0.196
r_symmetry_xyhbond_nbd_refined	0.193
r_symmetry_nbd_refined	0.178
r_xyhbond_nbd_refined	0.173
r_nbtor_refined	0.167
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2851
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms

Software

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