6ZM3 | pdb_00006zm3

The structure of an E2 ubiquitin-conjugating complex (UBC2-UEV1) essential for Leishmania amastigote differentiation

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1J7D	PDB ID: 1J7D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	UBC2 and UEV1 were mixed in a 1:1 molar ratio to a final concentration of 6.6 mg mL-1 and incubated on ice for 30 min. Crystals were grown using a sitting drop method with a 1:1 ratio of protein to reservoir solution (0.1 M Bis-Tris propane, pH 7.5, 0.2 M sodium formate and 20% PEG) in the drop. Crystals took 2 days to appear.

Crystal Properties
Matthews coefficient	Solvent content
2.16	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.523	α = 90
b = 72.568	β = 91.839
c = 120.094	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS EIGER2 XE 16M		2019-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976254	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.65	47.25	100	0.092	0.12	0.075	0.996	6.7	4.2		67149

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73			1.449	1.635	0.747	0.368		4.2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB ID: 1J7D	1.7	46.25	61440	3018	99.964	0.225	0.2228	0.22	0.2603	0.26	31.043

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]
1.251		-1.504	0.342		-1.494

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.496
r_dihedral_angle_4_deg	16.923
r_dihedral_angle_3_deg	16.909
r_dihedral_angle_1_deg	6.887
r_lrange_it	6.373
r_scangle_it	4.981
r_mcangle_it	3.658
r_scbond_it	3.458
r_mcbond_it	2.644
r_angle_refined_deg	1.564

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.496
r_dihedral_angle_4_deg	16.923
r_dihedral_angle_3_deg	16.909
r_dihedral_angle_1_deg	6.887
r_lrange_it	6.373
r_scangle_it	4.981
r_mcangle_it	3.658
r_scbond_it	3.458
r_mcbond_it	2.644
r_angle_refined_deg	1.564
r_nbtor_refined	0.315
r_symmetry_xyhbond_nbd_refined	0.283
r_symmetry_nbd_refined	0.21
r_nbd_refined	0.207
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.115
r_gen_planes_refined	0.009
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4622
Nucleic Acid Atoms
Solvent Atoms	267
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data reduction
Aimless	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.