8OG6

Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4PXW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.1M Tris pH 7.0, 2.13M Lithium acetate
Crystal Properties
Matthews coefficientSolvent content
2.7855.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.228α = 90
b = 82.228β = 90
c = 237.782γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.000SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.252.761000.99917.212.624916
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.270.717

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.24545.67723687113999.970.2040.20270.230847.665
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]
0.6350.3170.635-2.059
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.673
r_dihedral_angle_4_deg17.654
r_dihedral_angle_3_deg16.403
r_dihedral_angle_1_deg9.366
r_lrange_it8.188
r_lrange_other8.114
r_scangle_it4.462
r_scangle_other4.46
r_mcangle_it3.917
r_mcangle_other3.917
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.673
r_dihedral_angle_4_deg17.654
r_dihedral_angle_3_deg16.403
r_dihedral_angle_1_deg9.366
r_lrange_it8.188
r_lrange_other8.114
r_scangle_it4.462
r_scangle_other4.46
r_mcangle_it3.917
r_mcangle_other3.917
r_scbond_it2.846
r_scbond_other2.844
r_mcbond_it2.561
r_mcbond_other2.554
r_angle_refined_deg2.15
r_angle_other_deg1.427
r_nbd_refined0.215
r_nbd_other0.199
r_xyhbond_nbd_refined0.192
r_symmetry_nbd_other0.189
r_symmetry_nbd_refined0.189
r_nbtor_refined0.174
r_symmetry_xyhbond_nbd_refined0.142
r_chiral_restr0.096
r_symmetry_nbtor_other0.083
r_bond_refined_d0.02
r_gen_planes_refined0.013
r_gen_planes_other0.009
r_bond_other_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2385
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing