1V1F

Structure of the Arabidopsis thaliana SOS3 complexed with Calcium(II) and Manganese(II) ions


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.8PRIOR 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
Matthew coefficientSolvent content
3.4864.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.9α = 90
b = 91.9β = 90
c = 85.6γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002003-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM16ESRFBM16

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
134697.70.0864.54.570411.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.1697.70.511.54.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTSOS3 CA(II) COMPLEX, PDB ENTRY 1V1G320660936797.20.2380.2370.262RANDOM61.96
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]
-0.97-0.971.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.262
r_scangle_it4.142
r_scbond_it2.321
r_angle_refined_deg1.926
r_mcangle_it1.719
r_mcbond_it0.872
r_symmetry_vdw_refined0.377
r_nbd_refined0.261
r_symmetry_hbond_refined0.241
r_xyhbond_nbd_refined0.221
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.262
r_scangle_it4.142
r_scbond_it2.321
r_angle_refined_deg1.926
r_mcangle_it1.719
r_mcbond_it0.872
r_symmetry_vdw_refined0.377
r_nbd_refined0.261
r_symmetry_hbond_refined0.241
r_xyhbond_nbd_refined0.221
r_chiral_restr0.134
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_dihedral_angle_4_deg
r_nbtor_other
r_gen_planes_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_bond_other_d
r_symmetry_vdw_other
r_nbd_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbtor_refined
r_mcbond_other
r_dihedral_angle_3_deg
r_mcangle_other
r_dihedral_angle_2_deg
r_scbond_other
r_angle_other_deg
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 AtomsNumber
Protein Atoms1547
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing