4FJV | pdb_00004fjv

Crystal Structure of Human Otubain2 and Ubiquitin Complex

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TFF	1TFF and 3N32
experimental model	PDB	3N32	1TFF and 3N32

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	279	15 % (w/v) Polyethylene Glycol 3350, 0.1 M Magnesium Formate , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 279K

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.063	α = 90
b = 76.825	β = 90
c = 198.847	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 2M		2011-05-12	M	SINGLE WAVELENGTH
2	1	x-ray	100	PIXEL	DECTRIS PILATUS 2M		2011-05-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9173	Diamond	I04-1
2	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9173	Diamond	I04-1

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
1,2	2.047	50	99.1	0.168	11	9		52092		-1

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)
1,2	2.05	2.12	96.1		0.627	2.5	6.9	4955

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1TFF and 3N32	2.047	49.712	52002	2641	97.65	0.2088	0.2057	0.1991	0.2672	0.257	RANDOM

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]
-1.9217			3.726		-1.8043

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.912
f_angle_d	1.035
f_chiral_restr	0.075
f_bond_d	0.007
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5086
Nucleic Acid Atoms
Solvent Atoms	560
Heterogen Atoms	42

Software

Software
Software Name	Purpose
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling