3BYV

Crystal structure of Toxoplasma gondii specific rhoptry antigen kinase domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	20% PEG 3350, 0.2 M MgNO3, 0.1 M Tris-HCl pH 8.5, 1 mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2	VAPOR DIFFUSION, SITTING DROP	8.5	293	24% PEG 3350, 0.2 M MgNO3, 0.1 M Tris-HCl pH 8.5, 1 mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.072	α = 90
b = 69.821	β = 90
c = 85.418	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	CCD	ADSC QUANTUM 210		2007-06-24	M	SINGLE WAVELENGTH
2	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2007-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1		CHESS	A1
2	ROTATING ANODE	RIGAKU FR-E+ DW	2.29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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
1,2	1.8	40	99.9	0.069	0.06	28.5	7.3	33484	33484			24.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.86	100		0.486	0.427	4.21	7.4	3306

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	SAD	THROUGHOUT	1.8	36.44	31731	31731	1692	99.87	0.20334	0.20334	0.20172	0.2442	0.23273	0.2747	RANDOM	13.045

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]
-0.04			0.02		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.95
r_dihedral_angle_4_deg	19.926
r_dihedral_angle_3_deg	17.357
r_dihedral_angle_1_deg	8.639
r_scangle_it	4.75
r_scbond_it	3.289
r_angle_refined_deg	2.367
r_mcangle_it	2.056
r_mcbond_it	1.495
r_symmetry_hbond_refined	0.372
r_nbtor_refined	0.314
r_symmetry_vdw_refined	0.265
r_nbd_refined	0.226
r_xyhbond_nbd_refined	0.205
r_chiral_restr	0.189
r_bond_refined_d	0.028
r_gen_planes_refined	0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2846
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing