3I7B | pdb_00003i7b

Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with bumped kinase inhibitor NM-PP1

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, 0.18 M ammonium citrate, 4 mM NM-PP1; cryoprotected with 10% ethylene glycol, pH 6.5, sitting drop vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.243	α = 90
b = 72.851	β = 98.78
c = 65.713	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	0.97946	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	1.988	50	99.8	0.065	8.3	4.2		30350		5	29.7

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	1.988	2.06	98.1		0.741	1.9	4.1	2975

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	1.988	50	30333	1536	99.77	0.194	0.192	0.22	0.228	0.25	RANDOM	19.845

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]
0.34		0.78	0.67		-0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.84
r_dihedral_angle_4_deg	18.445
r_dihedral_angle_3_deg	12.534
r_dihedral_angle_1_deg	4.557
r_scangle_it	3.245
r_scbond_it	2.054
r_mcangle_it	1.724
r_mcbond_it	0.985
r_angle_refined_deg	0.878
r_angle_other_deg	0.749

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.84
r_dihedral_angle_4_deg	18.445
r_dihedral_angle_3_deg	12.534
r_dihedral_angle_1_deg	4.557
r_scangle_it	3.245
r_scbond_it	2.054
r_mcangle_it	1.724
r_mcbond_it	0.985
r_angle_refined_deg	0.878
r_angle_other_deg	0.749
r_mcbond_other	0.245
r_chiral_restr	0.05
r_bond_refined_d	0.006
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	3694
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	40

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.