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Human DHX9 in Complex with ATX968 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, HANGING DROP 298 0.2 M Lithium sulfate, 0.1 M MES pH 6.4, 20% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.82 56.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.875 α = 90 b = 85.875 β = 90 c = 350.085 γ = 90
Symmetry Space Group P 43 21 2
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 S 9M 2023-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.75 54.32 100 0.189 15.6 24.9 35391
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.88 100 1.687 2.4 25.5
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 2.75 54.32 33275 1800 99.41 0.2527 0.24976 0.25 0.30873 0.3088 RANDOM 68.056
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] 0.53 0.53 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.066 r_dihedral_angle_3_deg 13.886 r_dihedral_angle_4_deg 13.157 r_long_range_B_refined 5.505 r_long_range_B_other 5.48 r_dihedral_angle_1_deg 5.129 r_mcangle_it 3.2 r_mcangle_other 3.2 r_scangle_other 2.563 r_mcbond_it 1.813
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.066 r_dihedral_angle_3_deg 13.886 r_dihedral_angle_4_deg 13.157 r_long_range_B_refined 5.505 r_long_range_B_other 5.48 r_dihedral_angle_1_deg 5.129 r_mcangle_it 3.2 r_mcangle_other 3.2 r_scangle_other 2.563 r_mcbond_it 1.813 r_mcbond_other 1.813 r_scbond_it 1.407 r_scbond_other 1.403 r_angle_refined_deg 1.169 r_angle_other_deg 1.015 r_chiral_restr 0.035 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 6774 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 83
Software Software Software Name Purpose Aimless data reduction DIALS data scaling PHASER phasing REFMAC refinement