9BJU

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherinternal

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2770.1 mM sodium cacodylate pH 5.7, 15% PEG8000, 0.2 M magnesium acetate, 5 mM DTT
Crystal Properties
Matthews coefficientSolvent content
2.2946.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.297α = 90
b = 93.297β = 90
c = 362.757γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93PIXELDECTRIS PILATUS3 6M2018-05-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.97893SSRFBL19U1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.475099.90.1360.1420.044.513.158657
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)RedundancyNumber Unique Reflections (All)
12.472.561001.2281.2810.3580.83912.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.4748.8655496294299.640.22030.21840.25565RANDOM66.929
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]
1.71.7-3.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.503
r_dihedral_angle_4_deg20.007
r_dihedral_angle_3_deg16.506
r_dihedral_angle_1_deg7.209
r_long_range_B_refined5.245
r_long_range_B_other5.245
r_scangle_other2.628
r_mcangle_it2.585
r_mcangle_other2.585
r_scbond_it1.721
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.503
r_dihedral_angle_4_deg20.007
r_dihedral_angle_3_deg16.506
r_dihedral_angle_1_deg7.209
r_long_range_B_refined5.245
r_long_range_B_other5.245
r_scangle_other2.628
r_mcangle_it2.585
r_mcangle_other2.585
r_scbond_it1.721
r_scbond_other1.721
r_mcbond_it1.566
r_mcbond_other1.556
r_angle_refined_deg1.374
r_angle_other_deg0.856
r_chiral_restr0.064
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms10799
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms201

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing