7YPR

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

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293.15	18% PEG 6000, 0.1 M MES pH 6.5, 0.2 M Potassium chloride, and TCEP addictive

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.825	α = 90
b = 105.825	β = 90
c = 76.956	γ = 120

Symmetry
Space Group	P 32

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		2018-12-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	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	2.1	45.89	99.6	0.051	0.057	0.026	0.999	18.4	4.6		56839			25.7

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	2.1	2.16	100		0.225	0.256	0.121	0.954	7	4.4

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.101	45.866	55983	2800	99.653	0.183	0.1803	0.2281	43.165

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]
-0.002	-0.001		-0.002		0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.702
r_dihedral_angle_4_deg	16.867
r_dihedral_angle_3_deg	16.084
r_lrange_it	7.775
r_scangle_it	7.227
r_dihedral_angle_1_deg	6.48
r_scbond_it	6.173
r_mcangle_it	5.83
r_mcbond_it	5.168
r_angle_refined_deg	1.487
r_nbtor_refined	0.321
r_nbd_refined	0.218
r_symmetry_nbd_refined	0.206
r_ncsr_local_group_15	0.185
r_xyhbond_nbd_refined	0.183
r_ncsr_local_group_4	0.175
r_ncsr_local_group_11	0.168
r_ncsr_local_group_14	0.163
r_ncsr_local_group_9	0.162
r_ncsr_local_group_3	0.158
r_ncsr_local_group_5	0.157
r_ncsr_local_group_1	0.155
r_ncsr_local_group_13	0.154
r_ncsr_local_group_8	0.153
r_ncsr_local_group_12	0.15
r_symmetry_xyhbond_nbd_refined	0.149
r_ncsr_local_group_10	0.148
r_ncsr_local_group_7	0.147
r_ncsr_local_group_6	0.142
r_ncsr_local_group_2	0.141
r_metal_ion_refined	0.091
r_chiral_restr	0.074
r_bond_refined_d	0.01
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7210
Nucleic Acid Atoms
Solvent Atoms	427
Heterogen Atoms	13

Software

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