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Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound SRM-25-071
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, HANGING DROP 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 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 = 46.88 α = 90 b = 62.653 β = 90 c = 88.323 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 2019-10-17 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) 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 1.5 30 99.9 0.051 0.051 0.056 0.023 1 29.8 6 42517 -3 20.9
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 1.5 1.53 100 0.45 0.644 1.8 5.6
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 1.5 28.62 40217 2160 99.92 0.15929 0.15803 0.1581 0.18297 0.1832 RANDOM 24.997
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] 0.43 0.39 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 9.106 r_long_range_B_refined 7.288 r_long_range_B_other 6.925 r_scangle_other 5.037 r_dihedral_angle_1_deg 3.814 r_scbond_it 3.32 r_scbond_other 3.171 r_mcangle_it 2.718 r_mcangle_other 2.718 r_mcbond_it 1.796
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 9.106 r_long_range_B_refined 7.288 r_long_range_B_other 6.925 r_scangle_other 5.037 r_dihedral_angle_1_deg 3.814 r_scbond_it 3.32 r_scbond_other 3.171 r_mcangle_it 2.718 r_mcangle_other 2.718 r_mcbond_it 1.796 r_dihedral_angle_2_deg 1.783 r_mcbond_other 1.777 r_angle_refined_deg 1.441 r_angle_other_deg 0.441 r_chiral_restr 0.073 r_gen_planes_refined 0.018 r_gen_planes_other 0.015 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 247 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing