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Crystal Structure of human zipper-interacting protein kinase (ZIPK, alias DAPK3) in complex with a pyrazolo[3,4-d]pyrimidinone ligand (HS38)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P4F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 1.9 M Na2-Malonate, pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.33 47.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.492 α = 90 b = 98.491 β = 90.07 c = 115.022 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 93 PIXEL DECTRIS PILATUS 6M 2014-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97625 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.46 115.02 97 6.1 3.2 42067
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 FREE R-VALUE 1P4F 2.46 115.02 39975 2092 96.85 0.19001 0.18764 0.1925 0.237 0.2403 RANDOM 38.798
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] 0.5 1.81 -0.42 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.991 r_dihedral_angle_4_deg 18.42 r_dihedral_angle_3_deg 17.311 r_long_range_B_refined 6.186 r_long_range_B_other 6.157 r_dihedral_angle_1_deg 5.914 r_scangle_other 3.523 r_mcangle_it 2.931 r_mcangle_other 2.929 r_scbond_it 2.374
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.991 r_dihedral_angle_4_deg 18.42 r_dihedral_angle_3_deg 17.311 r_long_range_B_refined 6.186 r_long_range_B_other 6.157 r_dihedral_angle_1_deg 5.914 r_scangle_other 3.523 r_mcangle_it 2.931 r_mcangle_other 2.929 r_scbond_it 2.374 r_scbond_other 2.361 r_mcbond_it 1.798 r_mcbond_other 1.798 r_angle_refined_deg 1.737 r_angle_other_deg 1.018 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 8566 Nucleic Acid Atoms Solvent Atoms 476 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing