5AF6 | pdb_00005af6

Structure of Lys33-linked diUb bound to Trabid NZF1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UBQ	PDB ENTRIES 1UBQ AND 2WWZ
experimental model	PDB	2WWZ	PDB ENTRIES 1UBQ AND 2WWZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		20% PEG 550 MME, 10% PEG 20K, 0.12 M NA OXAMATE, 0.12 M NAF, 0.12 M NA CITRATE, 0.12 M NA/K TARTRATE 0.1 M MES/IMIDAZOLE PH 6.5

Crystal Properties
Matthews coefficient	Solvent content
3.99	69.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.384	α = 90
b = 126.512	β = 103.38
c = 78.092	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	110	PIXEL	DECTRIS PILATUS		2014-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24		Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	3.4	38.59	99.9	0.11	6.6	3.4		12855		2	83.17

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.4	3.67	100		0.56	2	3.4

Refinement

Statistics
Diffraction ID	Structure Solution 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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRIES 1UBQ AND 2WWZ	3.4	38.591	1.35	12783	643	99.43	0.1824	0.1803	0.18	0.2216	0.22	106.53

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	10.976
f_angle_d	0.603
f_chiral_restr	0.023
f_bond_d	0.002
f_plane_restr	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4076
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	5

Software

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