3GPE | pdb_00003gpe

Crystal Structure Analysis of PKC (alpha)-C2 domain complexed with Ca2+ and PtdIns(4,5)P2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DSY	C2 DOMAIN FROM PROTEIN KINASE C (ALPHA) COMPLEXED WITH CA2+ AND PHOSPHATIDYLSERINE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	20% PEG 8000, 50mM potassium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.848	α = 90
b = 57.848	β = 90
c = 90.479	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	96	CCD	ADSC QUANTUM 4		2007-09-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.9	30	99	0.06	13.3	4		14140	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	97.3		0.464	1.6

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	C2 DOMAIN FROM PROTEIN KINASE C (ALPHA) COMPLEXED WITH CA2+ AND PHOSPHATIDYLSERINE	2	20	11566	609	98.8	0.24434	0.24274	0.2429	0.2773	0.2845	RANDOM	16.343

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]
-0.08	-0.04		-0.08		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.332
r_dihedral_angle_3_deg	9.422
r_dihedral_angle_4_deg	8.357
r_dihedral_angle_1_deg	4.423
r_angle_refined_deg	0.707
r_scangle_it	0.641
r_scbond_it	0.384
r_mcangle_it	0.259
r_mcbond_it	0.131
r_chiral_restr	0.038

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.332
r_dihedral_angle_3_deg	9.422
r_dihedral_angle_4_deg	8.357
r_dihedral_angle_1_deg	4.423
r_angle_refined_deg	0.707
r_scangle_it	0.641
r_scbond_it	0.384
r_mcangle_it	0.259
r_mcbond_it	0.131
r_chiral_restr	0.038
r_bond_refined_d	0.002
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1124
Nucleic Acid Atoms
Solvent Atoms	92
Heterogen Atoms	32

Software

Software
Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	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.