6Z4J | pdb_00006z4j

A4V mutant of human SOD1 bound with benzyl benzoisoselenazolone derivative 5 in P21 space group

X-RAY DIFFRACTION

---

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, 2.5M ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.495	α = 90
b = 68.321	β = 106.362
c = 51.321	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	2020-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.55	36.964	99.8	0.042	0.058	0.04	0.998	11.6	3.2		36977			17.407

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	1.55	1.58	99.6		0.279	0.376	0.25	0.887	2	3.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1UXM	1.55	36.964	36948	1835	99.779	0.19	0.1891	0.2	0.2077	0.22	21.058

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]
1.165		-0.19	-0.987		-0.056

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.215
r_dihedral_angle_other_3_deg	35.286
r_dihedral_angle_4_deg	23.587
r_dihedral_angle_3_deg	14.367
r_dihedral_angle_1_deg	7.22
r_lrange_it	5.749
r_lrange_other	5.71
r_scangle_it	4.735
r_scangle_other	4.733
r_scbond_it	3.222
r_scbond_other	3.221
r_mcangle_it	2.833
r_mcangle_other	2.832
r_mcbond_it	2
r_mcbond_other	2
r_angle_refined_deg	1.746
r_angle_other_deg	1.577
r_symmetry_nbd_refined	0.352
r_nbd_other	0.282
r_nbd_refined	0.256
r_symmetry_nbd_other	0.197
r_metal_ion_refined	0.192
r_xyhbond_nbd_refined	0.182
r_symmetry_xyhbond_nbd_refined	0.167
r_nbtor_refined	0.16
r_ncsr_local_group_1	0.09
r_chiral_restr	0.085
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2201
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	42

Software

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