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Calcium-bound structure of calcium-dependent protein kinase 3 (CPK3) from Arabidopsis thaliana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LIJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 20% PEG3350, 0.2 M sodium/potassium tartrate tetrahydrate
Crystal Properties Matthews coefficient Solvent content 2.45 49.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.963 α = 90 b = 70.151 β = 90 c = 156.796 γ = 90
Symmetry Space Group P 21 21 21
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 2021-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.987 SSRF BL19U1
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 99.9 0.184 0.992 16 10.3 34440
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 2.18 1.258 0.808 2.1
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 2.105 44.451 34089 1693 96.389 0.207 0.2062 0.213 0.227 0.2357 39.76
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] -0.592 -0.08 0.672
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.488 r_dihedral_angle_3_deg 13.617 r_lrange_it 9.752 r_lrange_other 9.74 r_scangle_it 6.893 r_scangle_other 6.892 r_dihedral_angle_2_deg 6.115 r_dihedral_angle_1_deg 5.891 r_mcangle_it 4.586 r_mcangle_other 4.586
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.488 r_dihedral_angle_3_deg 13.617 r_lrange_it 9.752 r_lrange_other 9.74 r_scangle_it 6.893 r_scangle_other 6.892 r_dihedral_angle_2_deg 6.115 r_dihedral_angle_1_deg 5.891 r_mcangle_it 4.586 r_mcangle_other 4.586 r_scbond_it 4.445 r_scbond_other 4.444 r_mcbond_it 3.226 r_mcbond_other 3.217 r_angle_refined_deg 1.559 r_angle_other_deg 0.569 r_symmetry_nbd_refined 0.256 r_nbd_other 0.208 r_symmetry_nbd_other 0.197 r_nbd_refined 0.192 r_xyhbond_nbd_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.177 r_nbtor_refined 0.167 r_symmetry_xyhbond_nbd_other 0.092 r_chiral_restr 0.076 r_symmetry_nbtor_other 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3798 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling BALBES phasing