8J6G | pdb_00008j6g

Neutron structure of copper amine oxidase from Arthrobacter globiformis anaerobically reduced by phenylethylamine at pD 9.0

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3WA2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS		289	1.05 M potassium-sodium tartrate in 25 mM HEPES buffer, pH 7.4.

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.22	α = 90
b = 62.144	β = 112.22
c = 92.344	γ = 90

Symmetry
Space Group	C 1 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 PILATUS 6M		2018-05-22	M	SINGLE WAVELENGTH
2	1	neutron	100	DIFFRACTOMETER	iBIX		2018-04-05	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A
2	SPALLATION SOURCE	J-PARC MLF BEAMLINE BL-03	2.716-5.335	JPARC MLF	BL-03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	1.09	50	97.4	0.052		0.062		0.995		9.58	3.238		650618
2	1.67	21.37	96.9				0.1235			4.85	5.5811		92713

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.09	1.16		0.264		0.321		0.948
1	1.16	1.24		0.172		0.208		0.971
1	1.24	1.34		0.123		0.147		0.984
1	1.34	1.47		0.084		0.102		0.989
1	1.47	1.64		0.062		0.073		0.993
1	1.64	1.89		0.05		0.06		0.993
1	1.89	2.32		0.045		0.054		0.994
1	2.32	3.27		0.047		0.056		0.993
1	3.27	50		0.048		0.057		0.992

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.09	44.55				337074	4636	96.8		0.1518	0.1513	0.15	0.1608	0.16
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	1.67	21.37				92709		96.8		0.1995	0.1981		0.2252

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.786
f_angle_d	1.381
f_chiral_restr	0.102
f_plane_restr	0.011
f_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4876
Nucleic Acid Atoms
Solvent Atoms	1009
Heterogen Atoms	11

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
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.