2O25

Ubiquitin-Conjugating Enzyme E2-25 kDa Complexed With SUMO-1-Conjugating Enzyme UBC9

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YLA	PDB entries 1YLA and 1A3S
experimental model	PDB	1A3S	PDB entries 1YLA and 1A3S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	The protein complex (1:1) was dissolved at 26 mg/ml in 20 mM Tris-HCl, pH 8.0, 5% glycerol, 2 mM DTT. Hanging drops (2 microL + 2 microL), room temperature, well solution: 16% PEG MME 5000, 0.1 M bis-Tris, pH 6.0, 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.874	α = 85.05
b = 68.498	β = 80.85
c = 91.277	γ = 75.83

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	ADSC QUANTUM 210		2006-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.91841	CHESS	A1

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	2.6	30	93.3	0.051	13.9	1.9	27651	27651		-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)
1	2.6	2.64	70.8		0.293	2.17	1.7	1028

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 entries 1YLA and 1A3S	2.6	30	27651	26281	1398	92.92	0.23105	0.22775	0.29091	RANDOM	34.036

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]
-2.31	0.79	1.94	-2.91	-1.17	4.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.074
r_dihedral_angle_3_deg	20.218
r_dihedral_angle_4_deg	14.615
r_dihedral_angle_1_deg	5.437
r_scangle_it	1.693
r_angle_refined_deg	1.624
r_scbond_it	1.068
r_mcangle_it	0.636
r_mcbond_it	0.4
r_nbtor_refined	0.302
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.1
r_symmetry_hbond_refined	0.091
r_bond_refined_d	0.016
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5628
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms

Software

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