8ZD6 | pdb_00008zd6

Crystal structure of E40K variant of Cu/Zn-superoxide dismutase from dog (Canis familiaris) in the apo form complexed with 22E1 Fv-clasp

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold
experimental model	PDB	7WX0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	2% (v/v) polyethylene glycol 400, 0.1M HEPES sodium pH 7.5, 2.0M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.616	α = 90
b = 83.601	β = 94.52
c = 185.75	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		2023-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.900	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	3.29	47.83	99	0.055	1	7.8	3.4		38902

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.29	3.42			0.847	0.59	0.8

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3.29	43.94	36984	1918	98.98	0.27938	0.2769	0.2723	0.32642	0.3155	RANDOM	149.494

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]
20.31		4.14	-2.89		-17.85

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	28.717
r_long_range_B_other	28.717
r_scangle_other	21.159
r_mcangle_it	19.666
r_mcangle_other	19.665
r_dihedral_angle_3_deg	15.086
r_scbond_it	13.19
r_scbond_other	13.189
r_mcbond_it	12.534
r_mcbond_other	12.534
r_dihedral_angle_1_deg	6.767
r_dihedral_angle_2_deg	6.123
r_angle_refined_deg	0.978
r_angle_other_deg	0.35
r_chiral_restr	0.044
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12453
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
Coot	model building
XDS	data reduction