4EHP | pdb_00004ehp

Crystal Structure of human vinculin head domain (residues 1-252) in complex with alpha-catenin (residues 277-382)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IBF	pdb entry 2IBF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		295	PEG 3350, sodium acetate, VAPOR DIFFUSION, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.25	α = 90
b = 73.96	β = 90
c = 107.43	γ = 90

Symmetry
Space Group	P 21 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	MARMOSAIC 225 mm CCD		2010-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1	APS	22-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.655	107.432	100	0.089	0.068	21.2	7.2	13785	13785	1	1	58.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.65	2.8	100		0.485	0.485	1.6	7.3	1970

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 2IBF	2.66	22.71	13667	13637	686	100	0.247	0.1944	0.1925	0.2	0.2294	0.23	RANDOM	60.0904

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]
-12.478			6.1346		6.3435

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	3.32
t_omega_torsion	2.36
t_bcor	1.426
t_dihedral_angle_d	1.06
t_gen_planes	0.0126
t_bond_d	0.01
t_trig_c_planes	0.0067
t_cont
t_chiral

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2672
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	36

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
XSCALE	data scaling
BUSTER	refinement

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.