Experiment: 5XPE

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QT8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	Sodium-potassium phosphate, Sodium chloride, 1,6-Hexanediol

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.23	α = 90
b = 61.23	β = 90
c = 96.791	γ = 120

Symmetry
Space Group	P 32 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	293	CCD	RAYONIX MX225HE		2015-05-11	M	SINGLE WAVELENGTH
2	1	neutron	100	IMAGE PLATE	MAATEL IMAGINE		2014-12-17	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.0000	SPring-8	BL26B1
2	NUCLEAR REACTOR	ORNL High Flux Isotope Reactor BEAMLINE CG4D	3.3-4.5	ORNL High Flux Isotope Reactor	CG4D

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	1.648	46.505	99.9	0.053	0.053	0.057	0.018			65.2	10.8		25927
2	2.099	17.107	79.8	0.222	0.222	0.256	0.123			4.1	3.2		10108

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	1.65	1.71		0.527	0.527	0.562	0.192	0.917		5.3	8.5
2	2.1	2.21		0.332	0.332	0.396	0.211			2.2	2.6
2	2.21	2.35		0.337	0.337	0.393	0.196			2.1	2.9
2	2.35	2.51		0.32	0.32	0.372	0.185			2.1	3
2	2.51	2.71		0.305	0.305	0.36	0.187			2.2	2.8
2	2.71	2.97		0.263	0.263	0.309	0.159			2.6	2.9
2	2.97	3.32		0.245	0.245	0.286	0.144			2.8	3.1
2	3.32	3.83		0.214	0.214	0.245	0.117			3.1	3.5
2	3.83	4.7		0.193	0.193	0.217	0.097			3.2	4.1
2	4.7	6.64		0.173	0.173	0.195	0.086			3.4	4.2
2	6.64	17.107		0.096	0.096	0.113	0.058			5.5	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1.648	46.505		1.35		25888	1303	99.68		0.1565	0.155	0.1846	Random selection	39.71
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2.09	17.025				10107	513	78.35		0.2275	0.2247	0.278	Random selection

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	18.092
f_angle_d	1.432
f_chiral_restr	0.09
f_bond_d	0.016
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1312
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms	5

Software

Software
Software Name	Purpose
LAUEGEN	data processing
SCALA	data scaling
PDB_EXTRACT	data extraction
PHENIX	refinement
Coot	model building

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.