6Z3V | pdb_00006z3v

A4V mutant of human SOD1 bound with N-aryl benzoisoselenazolone derivative 13 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
2.04	39.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.07	α = 90
b = 68.09	β = 106.87
c = 50.86	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 PILATUS3 6M	mirrors	2020-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9686	Diamond	I24

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	1.25	39.6	92.3	0.078	0.106	0.072	0.999	8	3.2		69892			7.912

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	1.25	1.27	99.3		0.562	0.756	0.501	0.524	2.2	3.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1UXM	1.25	39.6	69865	3480	99.281	0.178	0.1776	0.19	0.1912	0.2	13.096

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]
0.224		0.196	-0.412		0.058

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.589
r_dihedral_angle_other_3_deg	21.389
r_dihedral_angle_4_deg	14.327
r_dihedral_angle_3_deg	11.76
r_dihedral_angle_1_deg	7.079
r_lrange_it	4.442
r_lrange_other	4.287
r_scangle_it	3.961
r_scangle_other	3.922
r_scbond_it	2.695
r_scbond_other	2.645
r_angle_refined_deg	1.901
r_mcangle_other	1.858
r_mcangle_it	1.856
r_angle_other_deg	1.571
r_mcbond_it	1.221
r_mcbond_other	1.221
r_symmetry_nbd_refined	0.293
r_nbd_refined	0.26
r_nbd_other	0.242
r_metal_ion_refined	0.209
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.155
r_symmetry_xyhbond_nbd_refined	0.147
r_ncsr_local_group_1	0.127
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_gen_planes_other	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2220
Nucleic Acid Atoms
Solvent Atoms	288
Heterogen Atoms	79

Software

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