4Y5Q | pdb_00004y5q

Activated Calcium-Dependent Protein Kinase 1 from Cryptosporidium parvum (CpCDPK1) in complex with AMP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	27% PEG 3350, 0.27 M ammonium tartrate (pH 7.0), 6% PEG 400, 5 mM TCEP, 4 mM MgCl2, 2 mM CaCl2, 2 mM AMP

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.07	α = 90
b = 55.89	β = 104.79
c = 81.45	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		2010-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.9797	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.994	40.272	97	0.064	0.085	0.043	8.5	3.8	34688	34688			31.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.99	2.1	95.1		0.651	0.651	0.419	1.2	3.9	4946

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2	39.38	32894	1734	96.71	0.1855	0.1832	0.19	0.2296	0.23	RANDOM	61.822

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]
0.28		-0.52	-2.56		2.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.226
r_dihedral_angle_4_deg	21.48
r_dihedral_angle_3_deg	16.577
r_dihedral_angle_1_deg	6.099
r_mcangle_it	4.542
r_mcbond_it	3.207
r_mcbond_other	3.194
r_angle_refined_deg	1.806
r_angle_other_deg	0.882
r_chiral_restr	0.106

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.226
r_dihedral_angle_4_deg	21.48
r_dihedral_angle_3_deg	16.577
r_dihedral_angle_1_deg	6.099
r_mcangle_it	4.542
r_mcbond_it	3.207
r_mcbond_other	3.194
r_angle_refined_deg	1.806
r_angle_other_deg	0.882
r_chiral_restr	0.106
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3602
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	27

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
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.