6L9C | pdb_00006l9c

Neutron structure of copper amine oxidase from Arthrobacter glibiformis at pD 7.4

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

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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	7.4	289	1.05M potassium-sodium tartrate, 25mM HEPES

Crystal Properties
Matthews coefficient	Solvent content
3	58.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.548	α = 90
b = 61.779	β = 112.13
c = 92.332	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	CCD	ADSC QUANTUM 315r		2016-05-31	M	SINGLE WAVELENGTH
2	1	neutron	100	PIXEL	DECTRIS PILATUS 6M	Ni-Ti supermirror neutron guide Detector: iBIXDetector type: WSF PSD (Wavelength Shift Fiber Position Sensitive Detector)	2015-11-10	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	3.0-5.7	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	1.14	50	99.4	0.069		0.076	0.029			14.8	5.2		296297			16.56
2	1.72	20.94	87.4				0.1249			4.99	2.6639		203273			16.56

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	1.14	1.16		0.801		0.95	0.504	0.703			3.5
1	1.16	1.18		0.71		0.841	0.446	0.746			3.5
1	1.18	1.2		0.629		0.746	0.394	0.775			3.5
1	1.2	1.23		0.553		0.654	0.344	0.828			3.5
1	1.23	1.25		0.494		0.584	0.307	0.862			3.5
1	1.25	1.28		0.433		0.511	0.269	0.889			3.6
1	1.28	1.32		0.375		0.443	0.233	0.912			3.6
1	1.32	1.35		0.314		0.371	0.194	0.932			3.6
1	1.35	1.39		0.264		0.311	0.163	0.951			3.6
1	1.39	1.44		0.223		0.263	0.138	0.964			3.6
1	1.44	1.49		0.186		0.22	0.115	0.973			3.6
1	1.49	1.55		0.149		0.176	0.093	0.981			3.5
1	1.55	1.62		0.148		0.163	0.067	0.988			5.6
1	1.62	1.7		0.128		0.138	0.052	0.992			7
1	1.7	1.81		0.104		0.113	0.043	0.994			6.9
1	1.81	1.95		0.085		0.093	0.037	0.994			6.6
1	1.95	2.15		0.081		0.086	0.028	0.996			9.6
1	2.15	2.46		0.071		0.075	0.025	0.996			9.5
1	2.46	3.09		0.063		0.067	0.024	0.996			9.1
1	3.09	50		0.056		0.062	0.027	0.992			6.3

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	1.14	45.03		1.33		296105	14805	99.28		0.1684	0.1677	0.1677	0.1815	0.1812		27.8236
NEUTRON DIFFRACTION		1.72	20.951				76237	3813	87.23		0.1815	0.18		0.2095

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	22.036
f_angle_d	1.318
f_chiral_restr	0.102
f_bond_d	0.009
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4890
Nucleic Acid Atoms
Solvent Atoms	2667
Heterogen Atoms	2

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing