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Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound SRM-26-100
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JKS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 Protein: 6.6 mg/ml, 0.25M Sodium chloride, 0.1M Tris-HCl (pH 8.0); Screen: 1.8M Ammomium sulfate, 0.2M Ammonium chloride; Soak: 24h, 1mM SRM-25-071, 10% DMSO, 1.8M Ammonium sulfate, 0.2M Ammonium chloride; Cryo: 1.8M Ammonium sulfate, 25% sucrose.
Crystal Properties Matthews coefficient Solvent content 1.92 35.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.95 α = 90 b = 62.52 β = 90 c = 88.22 γ = 90
Symmetry Space Group P 21 21 21
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 16M Bi-Morph KB Mirrors 2022-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12723 APS 21-ID-D
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 1.43 29.41 100 0.062 0.066 0.024 0.999 14 7.2 48766 20.81
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 1.43 1.47 100 0.889 0.959 0.356 0.761 2 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 1.43 28.61 46317 2384 99.92 0.13762 0.13557 0.1483 0.17647 0.1805 RANDOM 26.247
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] -1.79 1.52 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.159 r_dihedral_angle_1_deg 5.91 r_dihedral_angle_2_deg 5.561 r_rigid_bond_restr 4.194 r_long_range_B_refined 4.158 r_long_range_B_other 4.051 r_scangle_other 3.32 r_mcangle_it 2.958 r_mcangle_other 2.958 r_scbond_it 2.527
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.159 r_dihedral_angle_1_deg 5.91 r_dihedral_angle_2_deg 5.561 r_rigid_bond_restr 4.194 r_long_range_B_refined 4.158 r_long_range_B_other 4.051 r_scangle_other 3.32 r_mcangle_it 2.958 r_mcangle_other 2.958 r_scbond_it 2.527 r_scbond_other 2.512 r_mcbond_it 2.102 r_mcbond_other 2.102 r_angle_refined_deg 1.559 r_angle_other_deg 0.551 r_chiral_restr 0.091 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2270 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing