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Crystal structure of human DHX8 in complex with compound 51 and ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HYT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 0.5 microliter of DHX8del547 at 3 mg/mL with 1 mM ADP and 1 mM MgCl2, plus 1.5 microliter of a crystallisation solution consisting of 15% (v/v) MPD, 100 mM Sodium Acetate pH 5.5 and 6% (v/v) DMSO, against 250 microliter of crystallisation solution
Crystal Properties Matthews coefficient Solvent content 2.45 49.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.311 α = 90 b = 167.727 β = 92.61 c = 137.353 γ = 90
Symmetry Space Group P 1 21 1
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 CdTe 16M 2019-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9999 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.45 106.2 99.5 0.22 0.238 0.089 0.993 6.2 7.1 109277 55.75
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.49 99.5 2.454 2.648 0.987 0.341 7.1
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 2.45 35.8 109161 5418 99.4 0.2165 0.2146 0.209 0.252 0.2445 RANDOM 53.08
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] -8.9096 1.1488 3.1518 5.7578
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.88 t_omega_torsion 2.74 t_angle_deg 0.88 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.88 t_omega_torsion 2.74 t_angle_deg 0.88 t_bond_d 0.007 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19584 Nucleic Acid Atoms Solvent Atoms 817 Heterogen Atoms 408
Software Software Software Name Purpose BUSTER refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction DIALS data reduction