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Crystal structure of full-length human DCAF15-DDB1-deltaPBP-DDA1-RBM39 in complex with 4-(aminomethyl)-N-(3-cyano-4-methyl-1H-indol-7-yl)benzenesulfonamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UD7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 291.5 2% (v:v) TacsimateTM, pH 5.0, 0.1 M sodium citrate tribasic
676 dihydrate, pH 5.6, and 10-20% (w:v) polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.85 56.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.692 α = 90 b = 94.237 β = 90 c = 267.578 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 PIXEL DECTRIS PILATUS3 R CdTe 300K 2018-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 2.61 81.79 100 0.487 0.5 0.113 0.985 6.2 19.6 63346 44.13
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 2.61 2.69 100 3.221 3.309 0.752 0.326 19.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6UD7 2.61 78.13 63255 3190 99.6 0.241 0.239 0.2788 0.266 0.3068 RANDOM 75.62
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] 16.4534 -9.0551 -7.3984
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.34 t_omega_torsion 2.19 t_angle_deg 0.98 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.34 t_omega_torsion 2.19 t_angle_deg 0.98 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10698 Nucleic Acid Atoms Solvent Atoms 515 Heterogen Atoms 30
Software Software Software Name Purpose BUSTER refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction