3MDB | pdb_00003mdb

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

X-RAY DIFFRACTION

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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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.2262	0.277	0.278	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
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