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Cat DHX9 in Complex with Compound 23 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 7.8, 15% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.79 55.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.882 α = 90 b = 85.882 β = 90 c = 346.51 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 X 16M 2021-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03320 PETRA III, DESY P11
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 2.35 49.78 100 0.084 26.1 26.3 55489
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 2.35 2.42 100 1.877 2.3 25.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.35 49.78 52570 2791 99.96 0.20795 0.20512 0.26194 0.2518 RANDOM 69.143
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] -0.07 -0.07 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.075 r_dihedral_angle_4_deg 17.85 r_dihedral_angle_3_deg 16.313 r_long_range_B_refined 8.675 r_long_range_B_other 8.491 r_dihedral_angle_1_deg 6.917 r_scangle_other 2.552 r_mcangle_it 2.47 r_mcangle_other 2.47 r_scbond_it 1.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.075 r_dihedral_angle_4_deg 17.85 r_dihedral_angle_3_deg 16.313 r_long_range_B_refined 8.675 r_long_range_B_other 8.491 r_dihedral_angle_1_deg 6.917 r_scangle_other 2.552 r_mcangle_it 2.47 r_mcangle_other 2.47 r_scbond_it 1.727 r_scbond_other 1.604 r_angle_refined_deg 1.446 r_mcbond_it 1.428 r_mcbond_other 1.425 r_angle_other_deg 1.217 r_chiral_restr 0.066 r_bond_refined_d 0.007 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 6822 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 138
Software Software Software Name Purpose Aimless data reduction XDS data scaling PHASER phasing REFMAC refinement