3HX4 | pdb_00003hx4

Crystal structure of CDPK1 of Toxoplasma gondii, TGME49_101440, in presence of calcium

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	25 % PEG 3350, 0.2 M LiSO4, Tris-HCl pH 8.0, 2 mM AMPPNP, 2 mM CaCl2, 4 mM MgCl2, 6.25 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.236	α = 90
b = 95.605	β = 90
c = 101.612	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	IMAGE PLATE	RIGAKU RAXIS IV++		2009-05-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	1.85	50	99	0.063	0.046	31.262	5.5	41316	41316			33.9

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	1.85	1.92	90.8		0.997	0.842	1.23	2.8	3740

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.95	50	35714	35714	1806	99.93	0.212	0.209	0.2242	0.257	0.2689	RANDOM	26.256

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]
3.52			-1.23		-2.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.52
r_dihedral_angle_4_deg	17.995
r_dihedral_angle_3_deg	15.913
r_dihedral_angle_1_deg	5.424
r_scangle_it	2.274
r_scbond_it	1.423
r_angle_refined_deg	1.194
r_mcangle_it	0.879
r_mcbond_it	0.48
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3715
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms	72

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction