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Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound MW01-9-039SRM.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YPD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 292 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 MW01-9-039SRM, 10% DMSO, 1.8M Ammonium sulfate, 0.2M Ammonium chloride;
Cryo: 1.8M Ammonium sulfate, 25% sucrose.
Crystal Properties Matthews coefficient Solvent content 1.97 37.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.986 α = 90 b = 62.627 β = 90 c = 88.501 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 CCD MARMOSAIC 300 mm CCD 2020-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.9 30 100 0.122 0.122 0.049 0.991 18.3 7.2 21300 -3 25.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 100 0.551 0.661 2.3 6.6
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 1.9 29.52 20177 1046 99.93 0.15918 0.15735 0.1708 0.19671 0.2046 RANDOM 30.311
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] 1.74 -0.12 -1.62
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 8.84 r_long_range_B_other 8.566 r_dihedral_angle_3_deg 7.868 r_scangle_other 6.534 r_scbond_it 4.344 r_scbond_other 4.131 r_mcangle_it 3.585 r_mcangle_other 3.585 r_dihedral_angle_1_deg 3.386 r_mcbond_it 2.454
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 8.84 r_long_range_B_other 8.566 r_dihedral_angle_3_deg 7.868 r_scangle_other 6.534 r_scbond_it 4.344 r_scbond_other 4.131 r_mcangle_it 3.585 r_mcangle_other 3.585 r_dihedral_angle_1_deg 3.386 r_mcbond_it 2.454 r_mcbond_other 2.45 r_dihedral_angle_2_deg 2.031 r_angle_refined_deg 1.588 r_angle_other_deg 0.521 r_chiral_restr 0.085 r_gen_planes_refined 0.017 r_gen_planes_other 0.014 r_bond_refined_d 0.005 r_bond_other_d 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2238 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing