6ZHC

PROTAC6 mediated complex of VHL:EloB:EloC and Bcl-xL

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LM8	1LM8,1MAZ
experimental model	PDB	1MAZ	1LM8,1MAZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	291	0.2 M Potassium iodide, 0.1 M MES pH 6.5, 23% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.99	α = 90
b = 101.18	β = 90
c = 106.93	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS3 6M		2018-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	1.03320	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.92	47.27	99.9	0.079	15.1	6.5		59379

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.92	1.97	99.6		0.638	2.5	5.7

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1LM8,1MAZ	1.92	47.27	59378	2910	99.802	0.171	0.1694	0.1957	33.4

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]
0.019			-0.039		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.718
r_dihedral_angle_4_deg	19.674
r_dihedral_angle_3_deg	12.858
r_lrange_it	7.329
r_lrange_other	7.17
r_dihedral_angle_1_deg	6.418
r_scangle_it	5.205
r_scangle_other	5.204
r_mcangle_it	3.637
r_mcangle_other	3.636
r_scbond_it	3.296
r_scbond_other	3.295
r_mcbond_it	2.41
r_mcbond_other	2.406
r_angle_refined_deg	1.252
r_angle_other_deg	1.19
r_symmetry_xyhbond_nbd_other	0.313
r_symmetry_nbd_refined	0.219
r_nbd_other	0.212
r_nbd_refined	0.194
r_symmetry_nbd_other	0.175
r_xyhbond_nbd_refined	0.165
r_nbtor_refined	0.161
r_symmetry_xyhbond_nbd_refined	0.151
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.055
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3957
Nucleic Acid Atoms
Solvent Atoms	460
Heterogen Atoms	227

Software

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