Experiment: 3VQG

Crystal Structure Analysis of the PDZ Domain Derived from the Tight Junction Regulating Protein

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VWR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	30% polyethlene glycol monomethyl ether 5000, 0.2M ammonium sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.852	α = 90
b = 50.768	β = 120.08
c = 33.136	γ = 90

Symmetry
Space Group	C 1 2 1

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 270		2011-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-1A	1.0	Photon Factory	BL-1A

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	1.35	30	98.7	0.091		3.5	18907	18907		-3	14.67

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	1.35	1.37	99.7		0.991	43.8	3.5	952

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	2vwr	1.35	26.328	1.39	18907	18904	974	98.32	0.1718	0.1699	0.1611	0.2067	0.198	RANDOM	9.5138

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]
9.3562		5.2577	6.1693		10.3533

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.993
f_angle_d	1.032
f_chiral_restr	0.066
f_bond_d	0.005
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	700
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	5

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling