7GTF

PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000754b

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol

Crystal Properties
Matthews coefficient	Solvent content
3.38	63.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.465	α = 90
b = 90.465	β = 90
c = 106.917	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	PIXEL	DECTRIS PILATUS 6M		2016-09-25		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	1.97	63.195	95.8	0.118	0.132	0.996	11.02			66041		-3	38.332

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.97	2.09	97.8		1.451	1.607	0.526	1.29

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.97	45.23	32449	1333	93.44	0.2172	0.2155	0.2592	RANDOM	40.535

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]
0.2	0.1		0.2		-0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.571
r_dihedral_angle_4_deg	19.006
r_dihedral_angle_3_deg	14.464
r_dihedral_angle_1_deg	6.965
r_mcangle_it	4.701
r_mcbond_it	3.444
r_mcbond_other	3.356
r_angle_refined_deg	1.545
r_angle_other_deg	1.326
r_chiral_restr	0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.571
r_dihedral_angle_4_deg	19.006
r_dihedral_angle_3_deg	14.464
r_dihedral_angle_1_deg	6.965
r_mcangle_it	4.701
r_mcbond_it	3.444
r_mcbond_other	3.356
r_angle_refined_deg	1.545
r_angle_other_deg	1.326
r_chiral_restr	0.08
r_bond_refined_d	0.031
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2317
Nucleic Acid Atoms
Solvent Atoms	237
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
XDS	data reduction

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 R01GM133198.