Experiment: 7QPB

Catalytic C-lobe of the HECT-type ubiquitin ligase E6AP in complex with a hybrid foldamer-peptide macrocycle

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1C4Z	1C4Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	277	12% PEG 8000, 0.1 M sodium cacodylate, 0.1 M calcium acetate pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.91	α = 90
b = 59.05	β = 95.47
c = 67.3	γ = 90

Symmetry
Space Group	C 1 2 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 EIGER X 16M		2021-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9724	ESRF	ID23-1

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	2.342	29.53	98.35	0.06614	0.07841	0.04175	0.998	11.91	3.5		24491

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	2.342	2.426	97.05		0.6111	0.7249	0.3868	0.669	1.91	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1C4Z	2.342	29.53	1.36	24488	1225	98.41	0.2173	0.2149	0.2167	0.2626	0.2634

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
f_dihedral_angle_d	18.807
f_angle_d	0.62
f_chiral_restr	0.035
f_plane_restr	0.003
f_bond_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3381
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms	306

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction