6N6R

Crystal structure of ABIN-1 UBAN in complex with two M1-linked di-ubiquitins


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529830% v/v PEG-MME550, 0.1 M bis-tris pH 6.5, and 0.05 M calcium chloride dihydrate
Crystal Properties
Matthews coefficientSolvent content
2.3748.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.9α = 90
b = 88.18β = 90
c = 105.9γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702009-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1.00Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.9567.7699.70.0940.99715.17.136800
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)RedundancyNumber Unique Reflections (All)
11.9521000.8120.8533.17.2

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 REPLACEMENTTHROUGHOUT1.954834847189099.630.245290.243480.27786RANDOM37.042
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]
0.690.7-1.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.873
r_dihedral_angle_4_deg20.628
r_dihedral_angle_3_deg16.507
r_dihedral_angle_1_deg6.08
r_long_range_B_refined4.309
r_long_range_B_other4.282
r_mcangle_other2.039
r_mcangle_it2.039
r_scangle_other1.828
r_angle_refined_deg1.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.873
r_dihedral_angle_4_deg20.628
r_dihedral_angle_3_deg16.507
r_dihedral_angle_1_deg6.08
r_long_range_B_refined4.309
r_long_range_B_other4.282
r_mcangle_other2.039
r_mcangle_it2.039
r_scangle_other1.828
r_angle_refined_deg1.28
r_mcbond_other1.126
r_mcbond_it1.125
r_scbond_it0.963
r_scbond_other0.963
r_angle_other_deg0.903
r_chiral_restr0.074
r_bond_refined_d0.007
r_bond_other_d0.006
r_gen_planes_refined0.004
r_gen_planes_other0.001
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_scangle_it
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3518
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing