3DFA | pdb_00003dfa

Crystal structure of kinase domain of calcium-dependent protein kinase cgd3_920 from Cryptosporidium parvum

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QG5	PDB entry 2QG5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.6	293	0.1 M Tris-HCl pH 7.6, 20% PEG 8000, 0.38 M Ammonium sulfate, 25% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.447	α = 90
b = 69.447	β = 90
c = 137.414	γ = 90

Symmetry
Space Group	P 43 21 2

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 300 mm CCD		2008-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.91996	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.45	50	96.9	0.072	0.064	11.2	13.2	12641	12641			59.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.45	2.54	83.5		0.471	0.411	4.53	11.1	1058

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 2QG5	2.45	49.09	12590	12590	611	96.94	0.234	0.234	0.233	0.23	0.263	0.25	RANDOM	36.985

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]
-3.14			-3.14		6.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.021
r_dihedral_angle_3_deg	16.001
r_dihedral_angle_4_deg	15.833
r_dihedral_angle_1_deg	4.848
r_angle_refined_deg	1.014
r_scangle_it	0.926
r_scbond_it	0.586
r_mcangle_it	0.382
r_nbtor_refined	0.299
r_symmetry_hbond_refined	0.222

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.021
r_dihedral_angle_3_deg	16.001
r_dihedral_angle_4_deg	15.833
r_dihedral_angle_1_deg	4.848
r_angle_refined_deg	1.014
r_scangle_it	0.926
r_scbond_it	0.586
r_mcangle_it	0.382
r_nbtor_refined	0.299
r_symmetry_hbond_refined	0.222
r_mcbond_it	0.205
r_nbd_refined	0.18
r_xyhbond_nbd_refined	0.148
r_symmetry_vdw_refined	0.12
r_chiral_restr	0.064
r_bond_refined_d	0.007
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2104
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection

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.