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Crystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) in complex with FZ326
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6T29
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.9 293 0,1M NaCit, pH 5.9 2,1 M AmmSO4 0,1M Na/K tartrate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.809 α = 90 b = 45.948 β = 103.96 c = 108.535 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 EIGER X 16M 2022-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999990 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.95 42.15 95.5 0.09 0.097 0.037 0.999 15.2 7 19398
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 79.2 0.618 0.669 0.253 0.906 6.7
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 THROUGHOUT 6T29 1.95 42.15 18426 971 95.07 0.1681 0.1664 0.1794 0.2018 0.2079 RANDOM 29.298
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] 1.15 -0.94 1.57 -2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.737 r_dihedral_angle_2_deg 13.635 r_dihedral_angle_1_deg 6.241 r_angle_refined_deg 1.508 r_angle_other_deg 0.488 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2172 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 73
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing