3I3T

Crystal structure of covalent ubiquitin-USP21 complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IBI	PDB ENTRY 2IBI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	13% PEG 3350, 0.1 M Bis-Tris, 0.1 M Ammonium sulfate, 5 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.428	α = 88.71
b = 83.663	β = 75.73
c = 118.792	γ = 85.11

Symmetry
Space Group	P 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	CCD	MARMOSAIC 300 mm CCD		2008-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.97949	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.59	83.37	96.3	0.08	0.083	9.81	2.54	65088	65088

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.59	2.61	95.6		0.416	0.529	2.08	2.56

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 ENTRY 2IBI	2.59	83.37	61793	3293	95.8	0.18777	0.18614	0.21801	RANDOM	43.685

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]
-14.9	5.35	4.35	13.28	-24	1.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.513
r_dihedral_angle_4_deg	22.749
r_dihedral_angle_3_deg	22.173
r_dihedral_angle_1_deg	7.466
r_scangle_it	4.852
r_scbond_it	2.857
r_angle_refined_deg	1.998
r_mcangle_it	1.9
r_mcbond_it	0.978
r_chiral_restr	0.131
r_bond_refined_d	0.021
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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	12293
Nucleic Acid Atoms
Solvent Atoms	121
Heterogen Atoms	16

Software

Software
Software Name	Purpose
CBASS	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling