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Cat DHX9 in Complex with Compound 1 and ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8SZQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.15 M Ammonium sulfate, 0.1 M TRIS pH 8, 15% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.86 57.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.47 α = 90 b = 86.47 β = 90 c = 351.17 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 EIGER X 9M 2023-06-02 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) 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 2.27 48.52 99.97 0.123 0.999 18.5 25.5 59824
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.27 2.329 99.91 1.616 0.766 2.4 27.4
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 2.27 48.52 59824 3088 99.97 0.19712 0.19465 0.1988 0.24593 0.2472 RANDOM 53.724
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] 0.04 0.04 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.905 r_dihedral_angle_4_deg 17.301 r_dihedral_angle_3_deg 14.482 r_long_range_B_refined 8.761 r_long_range_B_other 8.755 r_scangle_other 6.64 r_dihedral_angle_1_deg 6.554 r_mcangle_other 5.661 r_mcangle_it 5.66 r_scbond_it 4.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.905 r_dihedral_angle_4_deg 17.301 r_dihedral_angle_3_deg 14.482 r_long_range_B_refined 8.761 r_long_range_B_other 8.755 r_scangle_other 6.64 r_dihedral_angle_1_deg 6.554 r_mcangle_other 5.661 r_mcangle_it 5.66 r_scbond_it 4.313 r_scbond_other 4.312 r_mcbond_it 3.839 r_mcbond_other 3.832 r_angle_refined_deg 1.405 r_angle_other_deg 1.206 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 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 6799 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement XDS data processing XDS data scaling PHASER phasing Coot model building Aimless data reduction