7PQ6

Crystal Structure of the Ring Nuclease 0811 mutant-S12A from Sulfolobus islandicus (Sis0811)

X-RAY DIFFRACTION

---

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
2.39	48.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.054	α = 90
b = 103.735	β = 102.99
c = 77.678	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		2020-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.00	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	2.67	60.82	98	0.945	6.7	6.3		16673

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	2.67	2.714			0.494

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	2.67	60.82	16225	839	95.531	0.223	0.22	0.2795	38.112

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]
-0.23		-0.068	-0.094		0.321

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.938
r_dihedral_angle_4_deg	24.812
r_dihedral_angle_3_deg	18.366
r_dihedral_angle_1_deg	7.436
r_lrange_it	5.784
r_lrange_other	5.784
r_mcangle_it	3.413
r_mcangle_other	3.413
r_scangle_it	2.996
r_scangle_other	2.996
r_mcbond_it	1.954
r_mcbond_other	1.952
r_scbond_it	1.726
r_scbond_other	1.725
r_angle_refined_deg	1.602
r_angle_other_deg	1.256
r_nbd_other	0.283
r_symmetry_nbd_refined	0.214
r_nbd_refined	0.205
r_symmetry_nbd_other	0.186
r_symmetry_xyhbond_nbd_refined	0.176
r_nbtor_refined	0.17
r_ncsr_local_group_1	0.155
r_xyhbond_nbd_refined	0.152
r_symmetry_xyhbond_nbd_other	0.101
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.07
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4440
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms

Software

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