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Crystal structure of DDB1 in complex with XS381952
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9BBG
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 2.62 53.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.64 α = 90 b = 124.7 β = 90 c = 167.716 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 2024-02-29 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 1.87 50 91.2 0.068 0.077 0.034 0.999 13.1 4.3 99776
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 1.87 1.9 94.1 0.94 1.051 0.46 0.666 4.7
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 FOURIER SYNTHESIS THROUGHOUT 1.87 25.1 94637 4984 91 0.16396 0.16107 0.1748 0.22024 0.2239 RANDOM 27.997
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] -2.61 2.93 -0.32
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 24.116 r_long_range_B_other 23.828 r_dihedral_angle_3_deg 12.222 r_scangle_other 10.815 r_mcangle_it 9.899 r_mcangle_other 9.899 r_dihedral_angle_2_deg 7.747 r_dihedral_angle_1_deg 7.69 r_scbond_it 7.415 r_scbond_other 7.267
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 24.116 r_long_range_B_other 23.828 r_dihedral_angle_3_deg 12.222 r_scangle_other 10.815 r_mcangle_it 9.899 r_mcangle_other 9.899 r_dihedral_angle_2_deg 7.747 r_dihedral_angle_1_deg 7.69 r_scbond_it 7.415 r_scbond_other 7.267 r_mcbond_it 6.557 r_mcbond_other 6.554 r_rigid_bond_restr 3.097 r_angle_refined_deg 1.282 r_angle_other_deg 0.446 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8705 Nucleic Acid Atoms Solvent Atoms 618 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling REFMAC phasing