3DL2

Hexagonal structure of the LDH domain of Human Ubiquitin-conjugating Enzyme E2-like Isoform A

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	290.9	1.6 M Sodium/potassium phosphate pH 6.5, 0.2 M Sodium chloride, 0.002 M Dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 290.9K

Crystal Properties
Matthews coefficient	Solvent content
3.23	61.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.603	α = 90
b = 105.603	β = 90
c = 131.918	γ = 120

Symmetry
Space Group	P 65

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	MAR CCD 165 mm		2006-08-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-BM		APS	17-BM

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	2.1	28	100	0.08	28.929	9.2		47978		-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)
	2.1	2.18	100		0.735	3.32	9

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 1I10	2.1	27.97	47978	45317	2402	98.88	0.1962	0.19463	0.2255	RANDOM	27.702

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]
1.48	0.74		1.48		-2.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.869
r_dihedral_angle_4_deg	20.368
r_dihedral_angle_3_deg	13.147
r_dihedral_angle_1_deg	4.914
r_scangle_it	1.892
r_scbond_it	1.143
r_angle_refined_deg	1.006
r_mcangle_it	0.68
r_mcbond_it	0.348
r_nbtor_refined	0.287
r_symmetry_vdw_refined	0.192
r_nbd_refined	0.184
r_symmetry_hbond_refined	0.135
r_xyhbond_nbd_refined	0.109
r_chiral_restr	0.067
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
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	4354
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms	17

Software

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