2G45

Co-crystal structure of znf ubp domain from the deubiquitinating enzyme isopeptidase T (isot) in complex with ubiquitin

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	300	16% polyethylene glycol 8000, 80 mM sodium cacodylate pH 6.5, 160 mM magenesium or calcium acetate, 20% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 300K, pH 6.50

Crystal Properties
Matthews coefficient	Solvent content
3.25	62.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.074	α = 90
b = 68.074	β = 90
c = 225.345	γ = 120

Symmetry
Space Group	P 64

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	MARRESEARCH		2005-07-09	M	SINGLE WAVELENGTH
2	1	x-ray		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0, 1.28317, 1.27163, 1.28855, 1.28237	APS	22-ID

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
2,1	1.99	35	99.9	0.087	13.9	10.4		40453		-3	23.9

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)
	1.99	2.06	100		0.367	7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2G43	1.99	35	40453	39760	3990	98.5	0.229	0.229	0.268	RANDOM	41.8

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]
5.52	1.93		5.52		-11.05

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.6
c_scangle_it	2.89
c_mcangle_it	2.02
c_scbond_it	1.88
c_angle_deg	1.3
c_mcbond_it	1.26
c_improper_angle_d	0.74
c_bond_d	0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3034
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms	3

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction