7OY0 | pdb_00007oy0

Structure of human Spermine Oxidase in complex with a highly selective allosteric inhibitor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	293	0.01 M Na Acet, 0.06 M NaF

Crystal Properties
Matthews coefficient	Solvent content
4.38	71.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 193.755	α = 90
b = 193.755	β = 90
c = 44.332	γ = 120

Symmetry
Space Group	P 3 2 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 EIGER X 16M		2020-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000040	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	2.09	167.8	48.2	0.068	0.068	18.9	13		27031

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.095	2.4	70		1.407	1.407	2	15.5

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	none	2.09	167.8	25687	1345	48.18	0.1968	0.1946	0.2	0.2385	0.24	RANDOM	68.76

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]
-0.42	-0.21		-0.42		1.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.477
r_dihedral_angle_4_deg	14.721
r_dihedral_angle_3_deg	14.562
r_dihedral_angle_1_deg	6.401
r_angle_refined_deg	1.372
r_angle_other_deg	1.127
r_chiral_restr	0.052
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.477
r_dihedral_angle_4_deg	14.721
r_dihedral_angle_3_deg	14.562
r_dihedral_angle_1_deg	6.401
r_angle_refined_deg	1.372
r_angle_other_deg	1.127
r_chiral_restr	0.052
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3621
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	81

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.