Experiment: 4P2A

Structure of mouse VPS26A bound to rat SNX27 PDZ domain

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DQO	PDB entries 3DQO and 2FAU.
experimental model	PDB	2FAU	PDB entries 3DQO and 2FAU.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	4 M NaCl, 0.1 M Na Citrate pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
3.62	66.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.81	α = 90
b = 113.81	β = 90
c = 94.771	γ = 120

Symmetry
Space Group	P 3 1 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	ADSC QUANTUM 210r		2013-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	1.008	Australian Synchrotron	MX1

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	2.7	68.3	100	0.105	14.8	12		19434

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB entries 3DQO and 2FAU.	2.7	56.905	1.9	19433	1949	99.96	0.2193	0.2149	0.2258	0.2585	0.2648

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.395
f_angle_d	1.357
f_chiral_restr	0.051
f_bond_d	0.011
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3072
Nucleic Acid Atoms
Solvent Atoms	35
Heterogen Atoms	2

Software

Software
Software Name	Purpose
PHENIX	refinement