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Crystal structure of human DHX9 in complex with ATX-968 and ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8SZP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 150 nanoliters of DHX9 at 10 mg/mL with 5 mM ADP, 5 mM MgCl2 and 90 micromolar ATX-968, plus 150 nanoliters of a crystallisation solution consisting of 100 mM Morpheus buffer system 2 pH 7-8, 100 mM Morpheus carboxylic acids mix and 30-40% Morpheus precipitant mix 2, plus 40 nanoliters of seeds, against 70 microliters of crystallisation solution
Crystal Properties Matthews coefficient Solvent content 3.2 61.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.611 α = 90 b = 166.973 β = 90 c = 293.495 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 EIGER2 XE 16M 2024-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 3.4 49.73 100 0.151 0.157 0.042 0.998 11.8 13.6 81625 117.5
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 3.4 3.46 100 3.612 3.747 0.994 0.5 14
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 3.4 49.73 81523 4130 100 0.2361 0.2349 0.2404 0.2583 0.2597 RANDOM 151.28
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] -10.7601 10.8467 -0.0867
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.24 t_omega_torsion 2.23 t_angle_deg 0.85 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 17.24 t_omega_torsion 2.23 t_angle_deg 0.85 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 24496 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 192
Software Software Software Name Purpose BUSTER refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction DIALS data reduction