Experiment: 6XEF

Crystal structure of the PTP1B YopH WPD loop Chimera 4 bound to vanadate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QKP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	277.15	tris hydrochloride pH 7.8, magnesium acetate tetrahydrate, PEG 8000 and benzamidine

Crystal Properties
Matthews coefficient	Solvent content
3.27	61.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.384	α = 90
b = 88.384	β = 90
c = 104.879	γ = 120

Symmetry
Space Group	P 31 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 315r		2019-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.97946	SSRL	BL9-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.048	50	99.8	0.142	0.146	0.035	7.5	16.4		30280

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.12	98.5		1.098	1.171	0.394	0.576		8.2

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	THROUGHOUT	3QKP	2.048	44.192	1.34	30249	1529	99.81	0.1825	0.1814	0.1827	0.2028	0.2038	49.3354

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2425
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	24

Software

Software
Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction