1V1F | pdb_00001v1f

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

X-RAY DIFFRACTION

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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

Symmetry
Space Group	I 41

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-Work (DCC)	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	0.23	0.262	0.22	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
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