9BJU

Crystal structure of the complex between VHL, ElonginB, ElonginC, and compound 5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		internal

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	0.1 mM sodium cacodylate pH 5.7, 15% PEG8000, 0.2 M magnesium acetate, 5 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.297	α = 90
b = 93.297	β = 90
c = 362.757	γ = 90

Symmetry
Space Group	P 41 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	PIXEL	DECTRIS PILATUS3 6M		2018-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97893	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.47	50	99.9	0.136	0.142	0.04	4.5	13.1		58657

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	2.47	2.56	100		1.228	1.281	0.358	0.839		12.5

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.47	48.86	55496	2942	99.64	0.2203	0.2184	0.25565	RANDOM	66.929

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]
1.7			1.7		-3.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.503
r_dihedral_angle_4_deg	20.007
r_dihedral_angle_3_deg	16.506
r_dihedral_angle_1_deg	7.209
r_long_range_B_refined	5.245
r_long_range_B_other	5.245
r_scangle_other	2.628
r_mcangle_it	2.585
r_mcangle_other	2.585
r_scbond_it	1.721
r_scbond_other	1.721
r_mcbond_it	1.566
r_mcbond_other	1.556
r_angle_refined_deg	1.374
r_angle_other_deg	0.856
r_chiral_restr	0.064
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10799
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	201

Software

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