3KU2 | pdb_00003ku2

Crystal Structure of inactivated form of CDPK1 from toxoplasma gondii, TGME49.101440

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HZT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	20% PEG 3350, 0.2 M KF, 2mM AMPPNP, 4 mM MgCl2, 6.25 mM TCEP, 30% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.01	α = 90
b = 72.912	β = 96.26
c = 65.018	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	RIGAKU SATURN A200		2009-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.54

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	2.3	50	99.5	0.059	0.048	8	3.5	20008	19908			56.66

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (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	3hzt	2.3	19.97	19889	19811	1009	99.61	0.1979	0.2	0.2365	0.25	RANDOM	55.17

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]
0.2685		0.5026	-0.0315		-0.237

RMS Deviations
Key	Refinement Restraint Deviation
o_angle_deg	1.09
o_bond_d	0.01
o_bond_d_na
o_bond_d_prot
o_angle_d
o_angle_d_na
o_angle_d_prot
o_angle_deg_na
o_angle_deg_prot
o_dihedral_angle_d
o_dihedral_angle_d_na
o_dihedral_angle_d_prot
o_improper_angle_d
o_improper_angle_d_na
o_improper_angle_d_prot
o_mcbond_it
o_mcangle_it
o_scbond_it
o_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3545
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	31

Software

Software
Software Name	Purpose
BUSTER	refinement
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
DENZO	data reduction