7PQA

Crystal Structure of the Ring Nuclease 0811 mutant-S12G/K169G from Sulfolobus islandicus (Sis0811)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7PQ2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	20% PEG 3350, 0.1M Bis-Tris propane pH 7.5, 0.2M KSCN

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.93	α = 90
b = 104.97	β = 102.89
c = 78.306	γ = 90

Symmetry
Space Group	C 1 2 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		2021-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.9779	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	2.04	76.38	97.6	0.99	18.5	7.1		38798

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	2.04	2.07			0.839

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	7PQ2	2.04	43.932	38244	1913	99.096	0.196	0.1942	0.2379	53.097

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]
0.007		-0.514	0.614		-0.349

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.476
r_dihedral_angle_4_deg	22.626
r_dihedral_angle_3_deg	17.624
r_lrange_it	8.777
r_lrange_other	8.777
r_dihedral_angle_1_deg	7.326
r_scangle_it	6.2
r_scangle_other	6.199
r_mcangle_it	5.123
r_mcangle_other	5.122
r_scbond_it	3.962
r_scbond_other	3.961
r_mcbond_it	3.397
r_mcbond_other	3.397
r_angle_refined_deg	1.86
r_angle_other_deg	1.431
r_nbd_refined	0.226
r_symmetry_nbd_refined	0.224
r_nbd_other	0.221
r_symmetry_nbd_other	0.186
r_xyhbond_nbd_refined	0.186
r_symmetry_xyhbond_nbd_refined	0.181
r_nbtor_refined	0.176
r_ncsr_local_group_1	0.157
r_symmetry_xyhbond_nbd_other	0.104
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4398
Nucleic Acid Atoms
Solvent Atoms	77
Heterogen Atoms

Software

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