6Z4M | pdb_00006z4m

A4V mutant of human SOD1 bound with 2-(pyridin-3-ylmethyl)benzoisoselenazolone derivative 10 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, 2.7M ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.411	α = 90
b = 68.002	β = 106.235
c = 50.903	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 PILATUS 6M-F	mirrors	2020-02-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9686	Diamond	I04-1

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	36.88	99.7	0.065	0.089	0.061	0.992	8.5	3.1		36425			16.089

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	99.7		0.422	0.571	0.381	0.798	2	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	1.55	36.88	36381	1810	99.63	0.196	0.1949	0.2	0.2078	0.21	22.696

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]
1.203		-0.068	-0.925		-0.204

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.693
r_dihedral_angle_4_deg	20.047
r_dihedral_angle_3_deg	13.995
r_dihedral_angle_1_deg	7.014
r_lrange_it	6.2
r_scangle_it	5.034
r_scbond_it	3.431
r_mcangle_it	3.309
r_mcbond_it	2.317
r_angle_refined_deg	1.682
r_nbtor_refined	0.313
r_symmetry_nbd_refined	0.309
r_nbd_refined	0.233
r_metal_ion_refined	0.231
r_symmetry_xyhbond_nbd_refined	0.168
r_xyhbond_nbd_refined	0.129
r_chiral_restr	0.122
r_ncsr_local_group_1	0.108
r_bond_refined_d	0.01
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2207
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms	49

Software

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