6Z4I

A4V mutant of human SOD1 bound with benzyl benzoisoselenazolone derivative 3 in P21 space group

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UXM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.7	292	100mM NaOAc pH 4.7, 150mM NaCl, 2.7M ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.334	α = 90
b = 68.26	β = 105.711
c = 50.706	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 EIGER2 XE 16M	mirrors	2019-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.8500	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.6	32.483	100	0.071	0.098	0.068	6.9	3.4		33208			21.834

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	1.6	1.63	99.8		0.398	0.541	0.364	0.774	2	3.4

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	1UXM	1.6	32.46	33183	1632	99.937	0.187	0.1858	0.2171	23.867

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]
0.86		-0.692	-0.55		0.068

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.385
r_dihedral_angle_other_3_deg	26.966
r_dihedral_angle_3_deg	14.978
r_dihedral_angle_4_deg	13.473
r_dihedral_angle_1_deg	13.003
r_lrange_it	5.295
r_lrange_other	5.295
r_scangle_it	4.052
r_scangle_other	4.051
r_mcangle_it	3.198
r_mcangle_other	3.198
r_scbond_it	2.727
r_scbond_other	2.726
r_mcbond_it	2.324
r_mcbond_other	2.299
r_angle_refined_deg	1.643
r_angle_other_deg	1.466
r_symmetry_nbd_refined	0.401
r_nbd_refined	0.289
r_nbd_other	0.22
r_metal_ion_refined	0.201
r_symmetry_nbd_other	0.191
r_symmetry_xyhbond_nbd_refined	0.162
r_nbtor_refined	0.155
r_xyhbond_nbd_refined	0.147
r_ncsr_local_group_1	0.121
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2222
Nucleic Acid Atoms
Solvent Atoms	217
Heterogen Atoms	79

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing