3NCG | pdb_00003ncg

Activated Calcium-Dependent Protein Kinase 1 from Cryptosporidium parvum (CpCDPK1) 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	3MWU	3mwu, 3igo
experimental model	PDB	3IGO	3mwu, 3igo

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	32% PEG 3350, 0.35 M di-ammonium tartrate (not pH'ed), 5 mM TCEP, 3 mM MgCl2, 1 mM CaCl2, 2 mM inhibitor, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.991	α = 90
b = 55.968	β = 104.78
c = 81.972	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	RIGAKU SATURN 944		2009-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

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	2.49	35	95.3	0.092	8.1	3.7		17762		5	52.9

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	2.49	2.59	97.2		0.649	2.1	3.7	1775

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	3mwu, 3igo	2.49	33.58	17724	907	94.82	0.253	0.25	0.25	0.305	0.3	RANDOM	58.73

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]
-1.75		0.64	-0.57		2.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.133
r_dihedral_angle_4_deg	18.018
r_dihedral_angle_3_deg	15.638
r_dihedral_angle_1_deg	5.672
r_scangle_it	4.361
r_scbond_it	2.906
r_mcangle_it	2.634
r_mcbond_it	1.555
r_angle_refined_deg	1.105
r_angle_other_deg	0.803

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.133
r_dihedral_angle_4_deg	18.018
r_dihedral_angle_3_deg	15.638
r_dihedral_angle_1_deg	5.672
r_scangle_it	4.361
r_scbond_it	2.906
r_mcangle_it	2.634
r_mcbond_it	1.555
r_angle_refined_deg	1.105
r_angle_other_deg	0.803
r_mcbond_other	0.342
r_chiral_restr	0.058
r_bond_refined_d	0.009
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	3418
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	27

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.