3N51 | pdb_00003n51

Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with bumped kinase inhibitor RM-1-95

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3I7B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	24% PEG 3350, 0.25 M ammonium citrate, 5 mM DTT, 2.3 mM RM-1-95; cryoprotected by quick dip into well soln + final conc. (4.5% SGPP buffer, 9% ethylene glycol, 2 mM RM-1-95), pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.523	α = 90
b = 72.754	β = 98.88
c = 66.024	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	ADSC QUANTUM 315r		2009-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.976	SSRL	BL7-1

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	2.1	50	99.9	0.094	6.6	3.8		26020		5	41.3

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)
	2.1	2.18	99.9		0.799	1.1	3.8	2590

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	FOURIER SYNTHESIS	THROUGHOUT	3i7b	2.1	39.45	26002	1325	99.88	0.196	0.193	0.2	0.242	0.24	RANDOM	50.291

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]
-0.1		0.87	0.41		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.67
r_dihedral_angle_4_deg	19.377
r_dihedral_angle_3_deg	14.053
r_dihedral_angle_1_deg	5.182
r_scangle_it	5.099
r_scbond_it	3.509
r_mcangle_it	2.747
r_mcbond_it	1.754
r_angle_refined_deg	1.124
r_angle_other_deg	0.801

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.67
r_dihedral_angle_4_deg	19.377
r_dihedral_angle_3_deg	14.053
r_dihedral_angle_1_deg	5.182
r_scangle_it	5.099
r_scbond_it	3.509
r_mcangle_it	2.747
r_mcbond_it	1.754
r_angle_refined_deg	1.124
r_angle_other_deg	0.801
r_mcbond_other	0.544
r_chiral_restr	0.062
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3613
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	36

Software

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

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.