5U4P

Protein-protein complex between 26S proteasome regulatory subunit RPN8, RPN11, and Ubiquitin S31

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4O8X	4O8X, 2ZNV, 4BOZ, 4JQW, 4K1R, rMSM, 4UN2
experimental model	PDB	2ZNV	4O8X, 2ZNV, 4BOZ, 4JQW, 4K1R, rMSM, 4UN2
experimental model	PDB	4BOZ	4O8X, 2ZNV, 4BOZ, 4JQW, 4K1R, rMSM, 4UN2
experimental model	PDB	4JQW	4O8X, 2ZNV, 4BOZ, 4JQW, 4K1R, rMSM, 4UN2
experimental model	PDB	4K1R	4O8X, 2ZNV, 4BOZ, 4JQW, 4K1R, rMSM, 4UN2
experimental model	PDB	4UN2	4O8X, 2ZNV, 4BOZ, 4JQW, 4K1R, rMSM, 4UN2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.8	291	1.5 M ammonium tartrate

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.21	α = 90
b = 126.21	β = 90
c = 139.87	γ = 120

Symmetry
Space Group	P 65 2 2

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		2015-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.1159	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.5	109.301	99	0.08667	1	30.3	19.2		23105

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4O8X, 2ZNV, 4BOZ, 4JQW, 4K1R, rMSM, 4UN2	2.5	109.301	1.34	23100	1156	98.9	0.2125	0.2113	0.2336

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	17.197
f_angle_d	1.198
f_chiral_restr	0.06
f_bond_d	0.015
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3250
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms	1

Software

Software
Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	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 R01GM133198.