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Co-crystal structure of human DDB1 bound to fragment UB028670
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E0C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 20% (v/w) PEG 3350, 0.2 M di-NH4tart
Crystal Properties Matthews coefficient Solvent content 2.61 52.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.924 α = 90 b = 125.268 β = 90 c = 168.529 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN A200 2021-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 46.82 99.4 0.11 0.117 0.041 0.999 16.7 8 90240
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) Redundancy Number Unique Reflections (All) 1 2 2.03 97.3 0.819 0.875 0.305 0.751 8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2 46.82 85778 4384 99.3 0.18992 0.1878 0.197 0.23191 0.2392 RANDOM 25.432
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 Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.349 r_dihedral_angle_1_deg 8.026 r_dihedral_angle_2_deg 7.372 r_long_range_B_refined 6.55 r_long_range_B_other 6.503 r_scangle_other 4.738 r_mcangle_it 3.573 r_mcangle_other 3.573 r_scbond_it 2.994 r_scbond_other 2.994
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.349 r_dihedral_angle_1_deg 8.026 r_dihedral_angle_2_deg 7.372 r_long_range_B_refined 6.55 r_long_range_B_other 6.503 r_scangle_other 4.738 r_mcangle_it 3.573 r_mcangle_other 3.573 r_scbond_it 2.994 r_scbond_other 2.994 r_mcbond_it 2.356 r_mcbond_other 2.353 r_angle_refined_deg 1.135 r_angle_other_deg 0.388 r_chiral_restr 0.056 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 8497 Nucleic Acid Atoms Solvent Atoms 642 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing