9BBH | pdb_00009bbh

Co-crystal structure of human DDB1 bound to fragment UB028670


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
2.6152.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.924α = 90
b = 125.268β = 90
c = 168.529γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002021-09-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.54

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
1246.8299.40.110.1170.0410.99916.7890240
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)
122.0397.30.8190.8750.3050.7518

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT246.8285778438499.30.189920.18780.20.231910.24RANDOM25.432
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]
0.64-0.62-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.349
r_dihedral_angle_1_deg8.026
r_dihedral_angle_2_deg7.372
r_long_range_B_refined6.55
r_long_range_B_other6.503
r_scangle_other4.738
r_mcangle_it3.573
r_mcangle_other3.573
r_scbond_it2.994
r_scbond_other2.994
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.349
r_dihedral_angle_1_deg8.026
r_dihedral_angle_2_deg7.372
r_long_range_B_refined6.55
r_long_range_B_other6.503
r_scangle_other4.738
r_mcangle_it3.573
r_mcangle_other3.573
r_scbond_it2.994
r_scbond_other2.994
r_mcbond_it2.356
r_mcbond_other2.353
r_angle_refined_deg1.135
r_angle_other_deg0.388
r_chiral_restr0.056
r_gen_planes_refined0.008
r_bond_refined_d0.007
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 Atoms8497
Nucleic Acid Atoms
Solvent Atoms642
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing