3I7C | pdb_00003i7c

Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with bumped kinase inhibitor NA-PP2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3I79

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop vapor diffusion	6.5	298	26% PEG 3350, 0.25 M ammonium citrate, 4 mM NA-PP2; directly frozen from mother liquor, pH 6.5, sitting drop vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.139	α = 90
b = 72.522	β = 103.76
c = 67.116	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	MARMOSAIC 325 mm CCD		2009-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97911	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	1.98	50	98.1	0.09	9.2	3.7		30803		3	26.6

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	1.98	2.06	96.6		0.702		3.6	2996

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	3I79	1.98	30	30780	1556	98.17	0.195	0.193	0.21	0.245	0.25	RANDOM	26.071

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]
0.45		0.24	-0.62		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.764
r_dihedral_angle_4_deg	16.923
r_dihedral_angle_3_deg	13.537
r_dihedral_angle_1_deg	4.659
r_scangle_it	4.492
r_scbond_it	2.85
r_mcangle_it	2.331
r_mcbond_it	1.385
r_angle_refined_deg	0.978
r_angle_other_deg	0.762

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.764
r_dihedral_angle_4_deg	16.923
r_dihedral_angle_3_deg	13.537
r_dihedral_angle_1_deg	4.659
r_scangle_it	4.492
r_scbond_it	2.85
r_mcangle_it	2.331
r_mcbond_it	1.385
r_angle_refined_deg	0.978
r_angle_other_deg	0.762
r_mcbond_other	0.383
r_chiral_restr	0.056
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3712
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms	24

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.