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Crystal structure of C-terminal truncated calcium-dependent protein kinase 3 (CPK3) from Arabidopsis thaliana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KU2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.2 M Na acetate trihydrate, 0.1 M Bis-Tris propane pH7.5, 20% w/v PEG3,350
Crystal Properties Matthews coefficient Solvent content 2.11 41.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.994 α = 106.062 b = 73.112 β = 102.404 c = 76.481 γ = 113.145
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 PILATUS3 6M 2019-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97852 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.1 50 96.8 0.046 0.999 17 3.4 62397
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 0.748 0.776
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.1 43.562 62390 3063 96.775 0.187 0.1851 0.1917 0.2312 0.2392 49.298
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] 2.456 -0.25 -0.141 -1.449 -1.82 1.452
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.525 r_dihedral_angle_6_deg 14.39 r_lrange_other 13.119 r_lrange_it 13.114 r_scangle_it 9.415 r_scangle_other 9.414 r_mcangle_it 7.345 r_mcangle_other 7.344 r_dihedral_angle_1_deg 6.402 r_scbond_it 6.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.525 r_dihedral_angle_6_deg 14.39 r_lrange_other 13.119 r_lrange_it 13.114 r_scangle_it 9.415 r_scangle_other 9.414 r_mcangle_it 7.345 r_mcangle_other 7.344 r_dihedral_angle_1_deg 6.402 r_scbond_it 6.253 r_scbond_other 6.253 r_dihedral_angle_2_deg 5.577 r_mcbond_it 5.157 r_mcbond_other 5.157 r_angle_refined_deg 1.556 r_angle_other_deg 0.52 r_nbd_refined 0.201 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.178 r_nbd_other 0.17 r_xyhbond_nbd_refined 0.144 r_symmetry_xyhbond_nbd_refined 0.114 r_chiral_restr 0.076 r_symmetry_nbtor_other 0.075 r_symmetry_nbd_refined 0.059 r_chiral_restr_other 0.041 r_symmetry_xyhbond_nbd_other 0.037 r_dihedral_angle_other_2_deg 0.017 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 7641 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing