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Crystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) bound to compound 19 (CS640)
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 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 = 57.64 α = 90 b = 45.62 β = 104.439 c = 108.949 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 2M 2017-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91840 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.55 33.8 86.2 0.996 10.9 4 34389
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 0.806
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2jc6 1.55 31.78 34359 1741 85.859 0.159 0.1573 0.1708 0.1829 0.1942 19.177
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] -0.359 -0.702 -0.26 0.866
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.29 r_dihedral_angle_4_deg 18.153 r_dihedral_angle_3_deg 12.889 r_dihedral_angle_1_deg 6.46 r_lrange_it 3.891 r_lrange_other 3.84 r_scangle_it 3.374 r_scangle_other 3.373 r_mcangle_it 3.136 r_mcangle_other 3.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.29 r_dihedral_angle_4_deg 18.153 r_dihedral_angle_3_deg 12.889 r_dihedral_angle_1_deg 6.46 r_lrange_it 3.891 r_lrange_other 3.84 r_scangle_it 3.374 r_scangle_other 3.373 r_mcangle_it 3.136 r_mcangle_other 3.135 r_scbond_it 2.834 r_scbond_other 2.833 r_mcbond_it 2.337 r_mcbond_other 2.336 r_rigid_bond_restr 1.865 r_angle_refined_deg 1.436 r_angle_other_deg 1.41 r_nbd_refined 0.21 r_nbd_other 0.192 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.173 r_symmetry_nbd_refined 0.163 r_xyhbond_nbd_refined 0.134 r_symmetry_xyhbond_nbd_refined 0.127 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2151 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing