2I6T

Orthorhombic Structure of the LDH domain of Human Ubiquitin-conjugating Enzyme E2-like Isoform A

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	26% PEG3350, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate, pH 5.2 in protein buffer comprising of 20 mM Tris-HCl, pH 8.0, 500 mM NaCl, 5% glycerol, 10 mM dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.088	α = 90
b = 98.912	β = 90
c = 126.753	γ = 90

Symmetry
Space Group	P 21 21 2

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++		2006-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54178

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	26.55	99.9	0.18	12.6	7	39716	39716		-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	2.1	2.18	100		0.72	2.88	6.6	3896

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	26.55	39715	37628	2086	99.82	0.18267	0.18019	0.23004	RANDOM	23.562

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.985
r_dihedral_angle_4_deg	24.017
r_dihedral_angle_3_deg	14.204
r_scangle_it	6.037
r_dihedral_angle_1_deg	5.676
r_scbond_it	4.026
r_mcangle_it	3.07
r_mcbond_it	2.077
r_angle_refined_deg	1.412
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.985
r_dihedral_angle_4_deg	24.017
r_dihedral_angle_3_deg	14.204
r_scangle_it	6.037
r_dihedral_angle_1_deg	5.676
r_scbond_it	4.026
r_mcangle_it	3.07
r_mcbond_it	2.077
r_angle_refined_deg	1.412
r_nbtor_refined	0.3
r_nbd_refined	0.215
r_symmetry_vdw_refined	0.157
r_xyhbond_nbd_refined	0.153
r_symmetry_hbond_refined	0.139
r_chiral_restr	0.092
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4281
Nucleic Acid Atoms
Solvent Atoms	277
Heterogen Atoms	62

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.