6Z4G | pdb_00006z4g

A4V mutant of human SOD1 bound with ebselen 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	39.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.95	α = 90
b = 67.72	β = 106.4
c = 50.65	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	0.9119	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	1.45	39.51	99.3	0.046	0.063	0.043	0.998	10.6	3.3		44399			16.111

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	1.45	1.47	99.8		0.585	0.787	0.523	0.686	1.8	3.4

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	1.45	39.51	44377	2259	99.211	0.158	0.1556	0.17	0.1933	0.2	21.212

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]
0.876		0.29	-1.496		0.383

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_3_deg	51.638
r_dihedral_angle_2_deg	36.722
r_dihedral_angle_3_deg	12.314
r_dihedral_angle_4_deg	10.52
r_dihedral_angle_1_deg	7.346
r_rigid_bond_restr	4.59
r_scangle_it	3.957
r_scbond_it	3.761
r_scbond_other	3.481
r_scangle_other	3.291
r_lrange_it	3.004
r_lrange_other	2.937
r_mcangle_it	2.212
r_mcangle_other	2.212
r_angle_refined_deg	2.205
r_mcbond_it	2.13
r_mcbond_other	2.13
r_angle_other_deg	1.663
r_symmetry_nbd_refined	0.377
r_nbd_other	0.286
r_symmetry_xyhbond_nbd_refined	0.285
r_nbd_refined	0.241
r_symmetry_nbd_other	0.202
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.13
r_ncsr_local_group_1	0.118
r_chiral_restr	0.105
r_symmetry_nbtor_other	0.091
r_bond_refined_d	0.039
r_gen_planes_refined	0.012
r_gen_planes_other	0.009
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2210
Nucleic Acid Atoms
Solvent Atoms	195
Heterogen Atoms	66

Software

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