5O6C

Crystal Structure of a threonine-selective RCR E3 ligase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.727723.3 mM Na2HPO4 23.3 mM (NH4)2SO4 23.3 mM NaNO3 18 % PEG500 MME 9 % PEG20000
Crystal Properties
Matthews coefficientSolvent content
3.3863.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.578α = 90
b = 82.578β = 90
c = 103.303γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.2823ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.754099.30.05118.36.94000718.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.7893.30.4042.43

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 DIFFRACTIONSADTHROUGHOUT1.75403914082399.310.172450.171920.1957RANDOM28.7
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]
-0.18-0.09-0.180.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.625
r_dihedral_angle_4_deg19.889
r_dihedral_angle_3_deg13.666
r_long_range_B_refined7.355
r_long_range_B_other7.32
r_dihedral_angle_1_deg6.447
r_scangle_other5.898
r_scbond_it3.862
r_scbond_other3.862
r_mcangle_other3.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.625
r_dihedral_angle_4_deg19.889
r_dihedral_angle_3_deg13.666
r_long_range_B_refined7.355
r_long_range_B_other7.32
r_dihedral_angle_1_deg6.447
r_scangle_other5.898
r_scbond_it3.862
r_scbond_other3.862
r_mcangle_other3.312
r_mcangle_it3.305
r_mcbond_it2.517
r_mcbond_other2.506
r_angle_refined_deg1.962
r_angle_other_deg0.979
r_chiral_restr0.115
r_bond_refined_d0.019
r_gen_planes_refined0.01
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 Atoms1980
Nucleic Acid Atoms
Solvent Atoms257
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
SHELXDphasing