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Structure of the Arabidopsis thaliana SOS3 complexed with Calcium(II) and Manganese(II) ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V1G SOS3 CA(II) COMPLEX, PDB ENTRY 1V1G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.8 PRIOR TO CRYSTALLIZATION THE PROTEIN WAS PREINCUBATED WITH 3.8 MM CACL2 PLUS 3.8 MM MNCL2 TO REACH A FINAL PROTEIN CONCENTRATION OF 10 MG/ML AND A PROTEIN:METAL ION RATIO 1:10:10. CRYSTALLIZATION EXPERIMENTS WERE CARRIED OUT AT ROOM TEMPERATURE. CRYSTALS WERE GROWN USING VAPOUR DIFFUSION TECHNIQUES FROM DROPS CONTAINING SOS3-CA-MN, RESERVOIR SOLUTIONS (24%(W/V) METHYL-PENTANEDIOL, 16%(W/V) POLYETHYLENE GLYCOL 4000 AND 0.1 NA-CITRATE PH 4.8) AND NAI 1M IN A RATIO 2:1:0.75
Crystal Properties Matthews coefficient Solvent content 3.48 64.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.9 α = 90 b = 91.9 β = 90 c = 85.6 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2003-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 ESRF BM16
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 46 97.7 0.086 4.5 4.5 7041 1.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.16 97.7 0.51 1.5 4.5
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 FOURIER SYNTHESIS THROUGHOUT SOS3 CA(II) COMPLEX, PDB ENTRY 1V1G 3 20 6609 367 97.2 0.238 0.237 0.262 0.2019 RANDOM 61.96
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] -0.97 -0.97 1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.262 r_scangle_it 4.142 r_scbond_it 2.321 r_angle_refined_deg 1.926 r_mcangle_it 1.719 r_mcbond_it 0.872 r_symmetry_vdw_refined 0.377 r_nbd_refined 0.261 r_symmetry_hbond_refined 0.241 r_xyhbond_nbd_refined 0.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.262 r_scangle_it 4.142 r_scbond_it 2.321 r_angle_refined_deg 1.926 r_mcangle_it 1.719 r_mcbond_it 0.872 r_symmetry_vdw_refined 0.377 r_nbd_refined 0.261 r_symmetry_hbond_refined 0.241 r_xyhbond_nbd_refined 0.221 r_chiral_restr 0.134 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1547 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling CCP4 phasing