Experiment: 9DNR

Structure of UBR2-RWF complex

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NY2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.3	293.15	For UBR2UBR-RWF co-crystal, the ligand to protein molar ratio is 1:5 and the reservoir contains 0.1 M Bis-Tris pH6.3 with 29% PEG 3350. The stock concentration of UBR2UBR for co-crystallization is 6.2 mg/ml.

Crystal Properties
Matthews coefficient	Solvent content
1.81	32.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.235	α = 90
b = 36.957	β = 109.56
c = 29.615	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	77	PIXEL	DECTRIS PILATUS3 6M		2022-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.97648	ALS	8.2.1

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	1.22	50	96.4	0.07	0.079	0.037	0.994	23.2	4.1		17252

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	1.22	1.24	81.2		0.173	0.197	0.093	0.951		3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	FREE R-VALUE	1.22	27.91	1.44	17238	866	96.91	0.1682	0.1676	0.1673	0.1799	0.1794

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	6.361
f_angle_d	0.955
f_chiral_restr	0.085
f_plane_restr	0.008
f_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	562
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	3

Software

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