6Z4K

A4V mutant of human SOD1 bound with benzyl benzoisoselenazolone derivative 6 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
2.02	39.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.24	α = 90
b = 68.32	β = 106.17
c = 50.98	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	2019-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

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	1.45	34.33	99.4	0.031	0.042	0.029	0.999	13.3	3.3		44385			16.64

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	1.45	1.47	99.4		0.561	0.769	0.524	0.609	1.4	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	1UXM	1.45	34.33	44362	2240	99.359	0.195	0.1947	0.2092	20.308

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]
1.43		-0.209	-0.963		-0.296

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.529
r_dihedral_angle_other_3_deg	32.139
r_dihedral_angle_4_deg	19.259
r_dihedral_angle_3_deg	13.311
r_dihedral_angle_1_deg	7.204
r_lrange_it	5.288
r_lrange_other	5.192
r_scangle_it	4.482
r_scangle_other	4.476
r_scbond_it	3.029
r_scbond_other	3.01
r_mcangle_it	2.664
r_mcangle_other	2.664
r_mcbond_it	1.913
r_mcbond_other	1.912
r_angle_refined_deg	1.747
r_angle_other_deg	1.644
r_symmetry_nbd_refined	0.341
r_nbd_refined	0.27
r_symmetry_xyhbond_nbd_refined	0.264
r_nbd_other	0.237
r_metal_ion_refined	0.228
r_symmetry_nbd_other	0.203
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.124
r_ncsr_local_group_1	0.1
r_chiral_restr	0.096
r_symmetry_nbtor_other	0.085
r_xyhbond_nbd_other	0.081
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2196
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	44

Software

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