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Crystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) in complex with FZ331
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 293 0,1M NaCit, pH 5.9 2,05M AmmSO4 0,1M Na/K tartrate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.531 α = 90 b = 44.8 β = 104.26 c = 108.589 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 1.7 44.95 96.3 0.037 0.04 0.015 0.999 21.5 7 28529
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 1.7 1.73 96.5 0.778 0.839 0.311 0.899 7.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6t29 1.7 44.95 27070 1427 95.85 0.2012 0.2 0.2242 0.2457 RANDOM 39.411
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] -0.21 -0.24 2.25 -1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.203 r_dihedral_angle_2_deg 7.802 r_dihedral_angle_1_deg 6.467 r_angle_refined_deg 1.318 r_angle_other_deg 0.437 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_bond_other_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2048 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 53
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing