8C13

Crystal structure of pVHL:ElonginC:ElonginB complex bound to PROTAC JW48

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	18% PEG 3350, HEPES pH7

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.797	α = 90
b = 60.787	β = 100.58
c = 97.228	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 PILATUS 2M-F		2021-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.999987	SLS	X06DA

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	2.3	48.833	99.1	0.111	0.121	0.046	0.997	9.9	7		18781

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	2.3	2.38		99.8	1.207	1.299	0.477	0.752		7.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.3	47.833	18775	921	98.909	0.225	0.2226	0.2612	57.148

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]
-2.992		-0.233	-0.663		3.498

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.6
r_dihedral_angle_3_deg	12.511
r_dihedral_angle_1_deg	6.136
r_lrange_it	3.21
r_lrange_other	3.209
r_dihedral_angle_2_deg	2.95
r_mcangle_it	1.867
r_mcangle_other	1.867
r_scangle_it	1.861
r_scangle_other	1.86
r_mcbond_it	1.082
r_mcbond_other	1.081
r_scbond_it	1.079
r_scbond_other	1.079
r_angle_refined_deg	0.756
r_angle_other_deg	0.277
r_symmetry_xyhbond_nbd_refined	0.204
r_nbd_refined	0.181
r_symmetry_nbd_other	0.172
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.144
r_nbd_other	0.099
r_symmetry_nbtor_other	0.075
r_symmetry_nbd_refined	0.069
r_chiral_restr	0.037
r_chiral_restr_other	0.019
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2704
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms	60

Software

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