☰ Navigation Tabs
Crystal structure of DDB1 in complex with XS445479
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9EJQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 20.0 P3350, 0.2 di-NH4tart
Crystal Properties Matthews coefficient Solvent content 2.64 53.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.544 α = 90 b = 124.709 β = 90 c = 168.627 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 2025-03-25 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 2.1 50 99.9 0.126 0.136 0.049 1 7.2 7.6 77601
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 2.1 2.14 100 0.963 1.037 0.383 0.715 7.2
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 2.1 27.97 73513 3841 99.41 0.20177 0.1988 0.2064 0.25959 0.2634 RANDOM 35.457
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] 0.4 0.26 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.161 r_dihedral_angle_2_deg 8.749 r_dihedral_angle_1_deg 8.218 r_long_range_B_refined 7.669 r_long_range_B_other 7.663 r_scangle_other 6.084 r_mcangle_it 5.064 r_mcangle_other 5.063 r_scbond_it 4.22 r_scbond_other 4.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.161 r_dihedral_angle_2_deg 8.749 r_dihedral_angle_1_deg 8.218 r_long_range_B_refined 7.669 r_long_range_B_other 7.663 r_scangle_other 6.084 r_mcangle_it 5.064 r_mcangle_other 5.063 r_scbond_it 4.22 r_scbond_other 4.22 r_mcbond_it 3.7 r_mcbond_other 3.696 r_angle_refined_deg 1.282 r_angle_other_deg 0.431 r_chiral_restr 0.062 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 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 8586 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction REFMAC phasing PDB_EXTRACT data extraction