3I79 | pdb_00003i79

Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop vapor diffusion	6.5	298	25% PEG 3350, 0.2 M tri-ammonium citrate; cryoprotected with 15% ethylene glycol, pH 6.5, sitting drop vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.144	α = 90
b = 71.861	β = 102.98
c = 67.265	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	CCD	MarUSA MarMosaic -325 CCD		2009-04-22		SAD
2	1	x-ray	100	CCD	MarUSA MarMosaic -325 CCD		2009-04-22		SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97923	SSRL	BL9-2
2	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97923	SSRL	BL9-2

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
1,2	2.04	50	99.9	0.052	10.4	4.2		28324		3	34.8

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)
1,2	2.04	2.12	100		0.67	2.2	4.2	2799

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 (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	2.04	36.89	28302	1431	99.66	0.215	0.213	0.2305	0.258	0.2739	RANDOM	30.032

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]
0.13		0.89	-0.7		0.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.314
r_dihedral_angle_4_deg	14.522
r_dihedral_angle_3_deg	13.157
r_dihedral_angle_1_deg	4.66
r_scangle_it	3.471
r_scbond_it	2.143
r_mcangle_it	2.025
r_mcbond_it	1.177
r_angle_refined_deg	0.866
r_angle_other_deg	0.769
r_mcbond_other	0.265
r_chiral_restr	0.05
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3650
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling