9BOL | pdb_00009bol

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		293	0.1 mM sodium cacodylate pH 5.7, 15% PEG8000, 0.2 M magnesium acetate, 5 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.46	α = 103.62
b = 47.74	β = 94.66
c = 100.35	γ = 98.33

Symmetry
Space Group	P 1

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		2018-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9792	APS	19-ID

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	1.99	46.66	91.4	0.048	12.6	3.7		52695

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.99	2.04			0.53	0.771		3.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.99	46.66	48292	2487	88.05	0.20394	0.20171	0.21	0.24791	0.25	RANDOM	42.831

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]
-1.19	-0.13	-1.33	2.57	-0.1	-0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.486
r_dihedral_angle_4_deg	18.752
r_dihedral_angle_3_deg	14.089
r_dihedral_angle_1_deg	6.67
r_long_range_B_refined	4.5
r_long_range_B_other	4.5
r_angle_refined_deg	1.224
r_angle_other_deg	1.087
r_mcangle_it	0.805
r_mcangle_other	0.805
r_scangle_other	0.791
r_mcbond_it	0.47
r_mcbond_other	0.47
r_scbond_it	0.467
r_scbond_other	0.467
r_chiral_restr	0.044
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
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	5467
Nucleic Acid Atoms
Solvent Atoms	349
Heterogen Atoms	104

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
STARANISO	data scaling
PHASER	phasing