4YJN | pdb_00004yjn

Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1639

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ONA	PDB entry 4ONA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	24% PEG 3350, 0.275 M ammonium citrate, 5 mM DTT, 2 mM UW1639

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.3	α = 90
b = 72.64	β = 99.72
c = 65.71	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	PIXEL	PSI PILATUS 6M		2014-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.9795	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	2.6	72.64	90.6	0.215	0.097	0.984	5.1	5.8		12536

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.72	92.4		1.749	0.801	0.402	1.1	5.5	1548

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 4ONA	2.6	64.77	11891	610	89.88	0.2164	0.2148	0.2179	0.249	0.2522	RANDOM	56.735

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]
-1.52		0.68	-1.32		2.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.567
r_dihedral_angle_4_deg	18.313
r_dihedral_angle_3_deg	17.73
r_dihedral_angle_1_deg	6.017
r_mcangle_it	2.33
r_angle_refined_deg	1.598
r_mcbond_it	1.358
r_mcbond_other	1.357
r_angle_other_deg	0.854
r_chiral_restr	0.104
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3668
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
Aimless	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing