9BBG

Co-crystal structure of human DDB1 bound to fragment UB028671


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3E0C 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29120% (v/w) PEG 3350, 0.2 M di-NH4tart
Crystal Properties
Matthews coefficientSolvent content
2.6453.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.139α = 90
b = 125.747β = 90
c = 169.512γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2021-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97911APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.747.0199.90.0660.0710.0260.99913.37.4148768
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)
11.71.731001.1141.1920.4220.6717.8

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 REPLACEMENTTHROUGHOUT1.747.01141317735099.920.184180.182410.2181RANDOM34.867
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]
0.27-0.08-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.224
r_dihedral_angle_2_deg8.269
r_long_range_B_refined7.701
r_long_range_B_other7.685
r_dihedral_angle_1_deg7.63
r_scangle_other6.59
r_mcangle_it4.711
r_mcangle_other4.711
r_scbond_it4.55
r_scbond_other4.549
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.224
r_dihedral_angle_2_deg8.269
r_long_range_B_refined7.701
r_long_range_B_other7.685
r_dihedral_angle_1_deg7.63
r_scangle_other6.59
r_mcangle_it4.711
r_mcangle_other4.711
r_scbond_it4.55
r_scbond_other4.549
r_mcbond_it3.467
r_mcbond_other3.465
r_angle_refined_deg1.343
r_angle_other_deg0.471
r_chiral_restr0.071
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms8532
Nucleic Acid Atoms
Solvent Atoms586
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing