3MDB

Crystal structure of the ternary complex of full length centaurin alpha-1, KIF13B FHA domain, and IP4

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3FM8	nearly isomorphous coordinates of PDB entry 3FM8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	291	Sample buffer: 20mM HEPES, pH 7.30, 500mM NaCl, 1mM TCEP, 5% Glycerol. Protein complex was mixed with PIP3 in 1:1 molar ratio and acetone (5%). Reservoir solution: 0.8M lithium sulfate, 0.5M ammonium sulfate, 0.1M sodium citrate. Cryo-protectant: 2.0M lithium sulfate., vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.66	58.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.797	α = 90
b = 115.797	β = 90
c = 189.269	γ = 90

Symmetry
Space Group	P 41 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	MAR300		2008-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.97625	APS	23-ID-B

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	2.95	30	100	0.139	6.4	14.6		27800

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	2.95	3.06	100		0.957		14.7	2716

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	nearly isomorphous coordinates of PDB entry 3FM8	2.952	29.437	27736	978	99.964	0.227	0.225	0.277	thin shells	51.231

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]
0.609			0.609		-1.218

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.67
r_dihedral_angle_4_deg	17.559
r_dihedral_angle_3_deg	15.777
r_dihedral_angle_1_deg	5.974
r_mcangle_it	1.994
r_scangle_it	1.421
r_angle_refined_deg	1.158
r_mcbond_it	1.136
r_scbond_it	0.86
r_angle_other_deg	0.806

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.67
r_dihedral_angle_4_deg	17.559
r_dihedral_angle_3_deg	15.777
r_dihedral_angle_1_deg	5.974
r_mcangle_it	1.994
r_scangle_it	1.421
r_angle_refined_deg	1.158
r_mcbond_it	1.136
r_scbond_it	0.86
r_angle_other_deg	0.806
r_mcbond_other	0.143
r_chiral_restr	0.068
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7066
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	41

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	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.