7YPP

Structural basis of a superoxide dismutase from a tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293.15	26% PEG 8000, 0.1 M MES pH 6.0, 0.2 M calcium acetate, TCEP addictive

Crystal Properties
Matthews coefficient	Solvent content
2.3	42.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.102	α = 94.895
b = 68.049	β = 108.385
c = 68.135	γ = 114.4

Symmetry
Space Group	P 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		2018-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	1.28	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.2	45.37	95.6	0.1	0.142	0.1	0.994	9.4	3.6		48587			27.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.27	93.1		0.677	0.957	0.677	0.596		3.3

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	1TO4	2.2	45.3	48420	2354	96.045	0.2	0.1981	0.2343	33.538

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]
0.01	-0.004	0.001	-0.006	-0.004	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.91
r_dihedral_angle_4_deg	14.92
r_dihedral_angle_3_deg	14.429
r_lrange_it	6.992
r_dihedral_angle_1_deg	6.577
r_scangle_it	4.499
r_mcangle_it	3.749
r_scbond_it	3.217
r_mcbond_it	2.502
r_angle_refined_deg	1.241
r_nbtor_refined	0.308
r_symmetry_nbd_refined	0.299
r_symmetry_xyhbond_nbd_refined	0.203
r_nbd_refined	0.199
r_xyhbond_nbd_refined	0.152
r_ncsr_local_group_7	0.105
r_ncsr_local_group_1	0.102
r_ncsr_local_group_9	0.102
r_ncsr_local_group_4	0.101
r_ncsr_local_group_13	0.101
r_ncsr_local_group_15	0.099
r_ncsr_local_group_6	0.098
r_ncsr_local_group_12	0.094
r_ncsr_local_group_3	0.093
r_ncsr_local_group_10	0.093
r_ncsr_local_group_11	0.093
r_chiral_restr	0.091
r_ncsr_local_group_2	0.089
r_ncsr_local_group_5	0.078
r_ncsr_local_group_14	0.076
r_ncsr_local_group_8	0.071
r_metal_ion_refined	0.066
r_bond_refined_d	0.008
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7069
Nucleic Acid Atoms
Solvent Atoms	498
Heterogen Atoms	14

Software

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