3LJU | pdb_00003lju

Crystal structure of full length centaurin alpha-1 bound with the head group of PIP3

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3FEH	pdb entry 3FEH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	20% PEG3350, 0.2M ammonium chloride. Protein buffer: 0.02M HEPES pH 7.3, 0.3M sodium chloride, 0.001M TCEP, 5% glyccerol, 2.0mg/mL L-alpha-Phosphatidyl-D-myo-inositol 3,4,5-triphosphate, dioctanoyl, from SIGMA, catalog no. P9953, vapor diffusion, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.727	α = 90
b = 66.414	β = 90
c = 127.219	γ = 90

Symmetry
Space Group	P 21 21 21

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 315		2008-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	APS	19-ID

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	1.7	50	98.8	0.108	9.1	4.3		48266

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)
	1.7	1.73	97.3		0.476		2.8	2338

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	pdb entry 3FEH	1.702	20	48202	2437	98.714	0.193	0.191	0.2	0.231	0.24	RANDOM	13.169

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]
-0.767			0.176		0.591

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.748
r_dihedral_angle_3_deg	12.401
r_dihedral_angle_4_deg	12.148
r_dihedral_angle_1_deg	6.067
r_scangle_it	4.585
r_mcangle_it	3.537
r_scbond_it	3.058
r_mcbond_it	2.414
r_angle_refined_deg	1.474
r_angle_other_deg	0.862

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.748
r_dihedral_angle_3_deg	12.401
r_dihedral_angle_4_deg	12.148
r_dihedral_angle_1_deg	6.067
r_scangle_it	4.585
r_mcangle_it	3.537
r_scbond_it	3.058
r_mcbond_it	2.414
r_angle_refined_deg	1.474
r_angle_other_deg	0.862
r_mcbond_other	0.816
r_chiral_restr	0.106
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3036
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms	53

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.