6Z4H | pdb_00006z4h

A4V mutant of human SOD1 bound with benzyl benzoisoselenazolone derivative 2 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, 2.6M ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.613	α = 90
b = 68.289	β = 105.759
c = 50.899	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		2020-02-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9795	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	1.95	39.84	99.7	0.065	0.091	0.063	0.985	7.4	3.1		18560			26.659

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	1.95	2	98.9		0.344	0.48	0.333	0.538	2.3	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	1.95	39.836	18533	871	99.586	0.222	0.221	0.23	0.242	0.25	29.501

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]
2.127		0.057	-1.631		-0.456

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_3_deg	57.119
r_dihedral_angle_2_deg	37.962
r_dihedral_angle_4_deg	19.931
r_dihedral_angle_3_deg	12.251
r_lrange_it	7.712
r_lrange_other	7.67
r_dihedral_angle_1_deg	7.657
r_scangle_it	5.514
r_scangle_other	5.381
r_scbond_it	3.92
r_scbond_other	3.78
r_mcangle_it	3.678
r_mcangle_other	3.676
r_mcbond_it	2.671
r_mcbond_other	2.67
r_angle_refined_deg	1.608
r_angle_other_deg	1.578
r_nbd_other	0.336
r_symmetry_nbd_refined	0.307
r_metal_ion_refined	0.256
r_nbd_refined	0.217
r_symmetry_nbd_other	0.209
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.141
r_symmetry_xyhbond_nbd_refined	0.103
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.086
r_ncsr_local_group_1	0.081
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2197
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	50

Software

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