Experiment: 5JPR

Neutron Structure of Compound II of Ascorbate Peroxidase

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XIF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	300	2.25 M Lithium sulfate, 0.1 M HEPES pH 8.3 - 8.9

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.095	α = 90
b = 82.095	β = 90
c = 75.162	γ = 90

Symmetry
Space Group	P 42 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	neutron	100	IMAGE PLATE	MAATEL IMAGINE	multilayer	2015-10-14	L	LAUE
2	1	x-ray	100	CCD	RIGAKU SATURN 944+	multilayer	2015-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	NUCLEAR REACTOR	ILL BEAMLINE LADI III	3.2 - 4.2	ILL	LADI III
2	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	2.2	40	69.8	0.18						7	4		9220
2	1.8	19.91	98.72	0.16						9.4	6.8		23857

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	1.806	19.91		1.36		23857	1194	98.72		0.1578	0.1547	0.1513	0.2159	0.2129
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2.202	36.714		2.03		9220	462	68.14		0.2401	0.2364		0.3104

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]
0.4889			0.4889		-0.9778
0.4889			0.4889		-0.9778

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.898
f_dihedral_angle_d	11.898
f_angle_d	1.366
f_angle_d	1.366
f_chiral_restr	0.115
f_chiral_restr	0.115
f_bond_d	0.016
f_bond_d	0.016
f_plane_restr	0.009
f_plane_restr	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1899
Nucleic Acid Atoms
Solvent Atoms	390
Heterogen Atoms	54

Software

Software
Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.