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Cat DHX9 in Complex with Compound 10 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, 20% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.79 55.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.73 α = 90 b = 85.73 β = 90 c = 348.48 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 2023-11-11 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 2.99 43.05 99.9 0.168 17.9 24.2 27613
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 2.99 3.17 99.6 1.186 2.9 19.1
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 2.99 42.9 26157 1357 99.78 0.22872 0.2262 0.2237 0.27682 0.2748 RANDOM 74.333
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] 1.7 1.7 -3.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.963 r_dihedral_angle_3_deg 13.689 r_dihedral_angle_4_deg 11.561 r_long_range_B_refined 5.339 r_long_range_B_other 5.307 r_dihedral_angle_1_deg 5.063 r_mcangle_it 3.193 r_mcangle_other 3.193 r_scangle_other 2.742 r_mcbond_it 1.841
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.963 r_dihedral_angle_3_deg 13.689 r_dihedral_angle_4_deg 11.561 r_long_range_B_refined 5.339 r_long_range_B_other 5.307 r_dihedral_angle_1_deg 5.063 r_mcangle_it 3.193 r_mcangle_other 3.193 r_scangle_other 2.742 r_mcbond_it 1.841 r_mcbond_other 1.837 r_scbond_it 1.526 r_scbond_other 1.526 r_angle_refined_deg 1.159 r_angle_other_deg 1.012 r_chiral_restr 0.034 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 6793 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 98
Software Software Software Name Purpose Aimless data reduction XDS data scaling PHASER phasing REFMAC refinement