6Z4L | pdb_00006z4l

A4V mutant of human SOD1 bound with 2-(pyridin-3-ylmethyl)benzoisoselenazolone derivative 9 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	39.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.93	α = 90
b = 67.49	β = 106.12
c = 50.78	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	1.5	34.69	95.2	0.058	0.079	0.054	0.994	9.7	3.5		38401			13.797

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	1.5	1.53	82		0.465	0.631	0.424	0.745	1.9	3.1

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	1.6	34.69	32156	1614	96.353	0.183	0.1819	0.18	0.2081	0.19	20.626

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]
1.531		0.522	-1.918		0.073

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.127
r_dihedral_angle_4_deg	23.29
r_dihedral_angle_3_deg	12.503
r_dihedral_angle_1_deg	7.238
r_lrange_it	5.159
r_scangle_it	4.799
r_scbond_it	3.275
r_mcangle_it	2.441
r_angle_refined_deg	1.754
r_mcbond_it	1.723
r_nbtor_refined	0.312
r_symmetry_nbd_refined	0.265
r_nbd_refined	0.23
r_symmetry_xyhbond_nbd_refined	0.23
r_ncsr_local_group_1	0.13
r_metal_ion_refined	0.126
r_chiral_restr	0.125
r_xyhbond_nbd_refined	0.092
r_bond_refined_d	0.011
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2221
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	53

Software

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