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Cat DHX9 in Complex with ATX968 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 298 0.15 M Ammonium sulfate, 0.1 M TRIS pH 8, 15% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.86 57.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.45 α = 90 b = 86.45 β = 90 c = 351.04 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 2.43 54.5 100 0.141 19.3 25.2 51611
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 2.43 2.5 100 1.953 2 22.1
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 2.43 54.5 48991 2496 99.97 0.19707 0.19446 0.1984 0.24616 0.2494 RANDOM 56.293
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] 0.03 0.03 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.556 r_dihedral_angle_4_deg 17.996 r_dihedral_angle_3_deg 15.79 r_long_range_B_refined 9.536 r_long_range_B_other 9.531 r_scangle_other 7.129 r_dihedral_angle_1_deg 6.676 r_mcangle_other 5.96 r_mcangle_it 5.959 r_scbond_it 4.606
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.556 r_dihedral_angle_4_deg 17.996 r_dihedral_angle_3_deg 15.79 r_long_range_B_refined 9.536 r_long_range_B_other 9.531 r_scangle_other 7.129 r_dihedral_angle_1_deg 6.676 r_mcangle_other 5.96 r_mcangle_it 5.959 r_scbond_it 4.606 r_scbond_other 4.572 r_mcbond_it 4.012 r_mcbond_other 4.007 r_angle_refined_deg 1.422 r_angle_other_deg 1.202 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 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 6798 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 104
Software Software Software Name Purpose Aimless data reduction XDS data scaling PHASER phasing REFMAC refinement