3ZNZ | pdb_00003znz

Crystal structure of OTULIN OTU domain (C129A) in complex with Met1- di ubiquitin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZNV	PDB ENTRY 3ZNV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		100 MM BIS-TRIS, 2M (NH4)2SO4, PH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.02	α = 90
b = 100.02	β = 90
c = 280.26	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	287	CCD	ADSC CCD	MIRROR	2012-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04		Diamond	I04

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	1.9	42.8	100	0.09	14.4	8.9		42974		2	27.36

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	1.9	2	100		0.78	3	9.1

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 ENTRY 3ZNV	1.9	42.802	1.34	42965	2168	99.97	0.1857	0.1839	0.184	0.222	0.2216

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]
4.4091			4.4091		-8.8181

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.864
f_angle_d	1.018
f_chiral_restr	0.07
f_bond_d	0.007
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3294
Nucleic Acid Atoms
Solvent Atoms	370
Heterogen Atoms	35

Software

Software
Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALEPACK	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.