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Crystal structure of inactive 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 20% PEG500MME, 10% PEG20000, 0.1 M Buffer System2 pH7.5 (directly mixed by HEPES-Na and MOPS), 0.02 M sodium formate, 0.02 M NH4Ac, 0.02 M sodium citrate, 0.02 M sodium/potassium tartrate, 0.02 M sodium oxamate
Crystal Properties Matthews coefficient Solvent content 2.77 55.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.307 α = 90 b = 225.091 β = 95.883 c = 77.446 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 6M 2020-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.987 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 3.05 50 100 0.125 0.994 13.99 5.7 50680
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 3.05 3.16 1.025 0.62 1.72
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 3.05 40.2 48950 2472 96.351 0.214 0.213 0.2144 0.241 0.237 83.52
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] -0.013 -0.169 0.011 0.036
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.439 r_lrange_other 17.439 r_dihedral_angle_3_deg 16.395 r_dihedral_angle_6_deg 15.003 r_scangle_it 11.156 r_scangle_other 11.155 r_mcangle_it 11.096 r_mcangle_other 11.096 r_mcbond_it 7.137 r_mcbond_other 7.131
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.439 r_lrange_other 17.439 r_dihedral_angle_3_deg 16.395 r_dihedral_angle_6_deg 15.003 r_scangle_it 11.156 r_scangle_other 11.155 r_mcangle_it 11.096 r_mcangle_other 11.096 r_mcbond_it 7.137 r_mcbond_other 7.131 r_scbond_it 6.986 r_scbond_other 6.986 r_dihedral_angle_1_deg 6.336 r_dihedral_angle_2_deg 3.748 r_angle_refined_deg 1.485 r_angle_other_deg 0.517 r_nbd_other 0.23 r_symmetry_nbd_other 0.205 r_symmetry_nbd_refined 0.172 r_nbtor_refined 0.171 r_nbd_refined 0.17 r_xyhbond_nbd_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.162 r_chiral_restr_other 0.111 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.07 r_symmetry_xyhbond_nbd_other 0.028 r_dihedral_angle_other_2_deg 0.024 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15020 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing