2IBI

Covalent Ubiquitin-USP2 Complex

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		9	298	22% PEG1500, 0.1 M Bicine, 0.2 M NaCl, 1 mM DTT, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 9.00

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.839	α = 90
b = 54.4	β = 107.66
c = 75.021	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	100	IMAGE PLATE	RIGAKU RAXIS IV		2006-09-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	28.01	96.4	0.158	10.32	4.7		19694		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.2	2.24	70.7		0.65	1.5	1.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 2GFO, 1UBQ	2.2	28.01	18491	1002	96.26	0.19352	0.18989	0.25887	RANDOM	46.287

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]
-1.07		0.21	0.5		0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.189
r_dihedral_angle_4_deg	20.757
r_dihedral_angle_3_deg	17.156
r_dihedral_angle_1_deg	6.696
r_scangle_it	5.31
r_scbond_it	3.58
r_mcangle_it	2.839
r_mcbond_it	1.757
r_angle_refined_deg	1.399
r_nbtor_refined	0.307
r_symmetry_hbond_refined	0.242
r_symmetry_vdw_refined	0.216
r_nbd_refined	0.205
r_xyhbond_nbd_refined	0.159
r_chiral_restr	0.104
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3318
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing