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Crystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) bound to compound 18 (CS587)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JC6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.9 293 0,1M NaCit, pH 5.9
2,05M AmmSO4
0,1M Na/K tartrate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.82 α = 90 b = 45.64 β = 104.183 c = 108.754 γ = 90
Symmetry Space Group I 1 2 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 PILATUS 6M 2017-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.95372 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.48 55.45 98.7 0.026 0.999 14.8 6.3 44955
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 1.48 1.51 98.3 0.155 0.883 4.2 6.6
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2jc6 1.484 55.448 44954 2291 98.465 0.137 0.1355 0.1747 0.1892 17.818
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] 0.727 -0.17 -0.188 -0.402
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.006 r_dihedral_angle_4_deg 21.923 r_dihedral_angle_3_deg 11.751 r_dihedral_angle_1_deg 6.255 r_lrange_it 3.535 r_lrange_other 3.535 r_scangle_it 2.815 r_scangle_other 2.815 r_mcangle_it 2.324 r_mcangle_other 2.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.006 r_dihedral_angle_4_deg 21.923 r_dihedral_angle_3_deg 11.751 r_dihedral_angle_1_deg 6.255 r_lrange_it 3.535 r_lrange_other 3.535 r_scangle_it 2.815 r_scangle_other 2.815 r_mcangle_it 2.324 r_mcangle_other 2.323 r_scbond_it 2.231 r_scbond_other 2.23 r_mcbond_it 1.714 r_mcbond_other 1.713 r_angle_other_deg 1.416 r_angle_refined_deg 1.409 r_rigid_bond_restr 1.4 r_nbd_refined 0.215 r_symmetry_nbd_refined 0.187 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.174 r_nbd_other 0.163 r_symmetry_xyhbond_nbd_refined 0.136 r_xyhbond_nbd_refined 0.127 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2175 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing