7GTP | pdb_00007gtp

PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000688a

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
3.36	63.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.097	α = 90
b = 90.097	β = 90
c = 107.174	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	2.47	78.027	99.9	0.155	0.172	0.994	9.04			34838		-3	45.96

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	2.47	2.62	99.6		0.908	1.009	0.508	1.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.47	78.03	17761	725	99.95	0.1981	0.1958	0.26	0.2522	0.29	RANDOM	43.694

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]
0.16	0.08		0.16		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.754
r_dihedral_angle_4_deg	16.577
r_dihedral_angle_3_deg	16.408
r_dihedral_angle_1_deg	6.473
r_mcangle_it	3.989
r_mcbond_other	2.749
r_mcbond_it	2.748
r_angle_refined_deg	1.352
r_angle_other_deg	1.24
r_chiral_restr	0.064

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.754
r_dihedral_angle_4_deg	16.577
r_dihedral_angle_3_deg	16.408
r_dihedral_angle_1_deg	6.473
r_mcangle_it	3.989
r_mcbond_other	2.749
r_mcbond_it	2.748
r_angle_refined_deg	1.352
r_angle_other_deg	1.24
r_chiral_restr	0.064
r_bond_refined_d	0.039
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2427
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	253

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 R01GM157729.