5JNT

Crystal structure of human low molecular weight protein tyrosine phosphatase (LMPTP) type A complexed with MES

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	6.5	293	20% PEG 3350, 200 mM NaCl, 40 mM MES

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.905	α = 90
b = 55.018	β = 90
c = 96.423	γ = 90

Symmetry
Space Group	P 21 21 21

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 315		2015-08-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 12.3.1	1.0781	ALS	12.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.36	33.9	97.8	0.039	0.999	25	5.9		38952

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	1.36	1.38	72.7		0.227		1.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	5JNR	1.45	33.9	31159	1610	99.83	0.1362	0.1346	0.1658	RANDOM	15.964

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]
-0.07			0.03		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.386
r_dihedral_angle_4_deg	15.166
r_dihedral_angle_3_deg	11.764
r_dihedral_angle_1_deg	6.296
r_angle_refined_deg	3.023
r_mcangle_it	2.306
r_mcbond_it	1.49
r_mcbond_other	1.478
r_angle_other_deg	1.275
r_chiral_restr	0.387

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.386
r_dihedral_angle_4_deg	15.166
r_dihedral_angle_3_deg	11.764
r_dihedral_angle_1_deg	6.296
r_angle_refined_deg	3.023
r_mcangle_it	2.306
r_mcbond_it	1.49
r_mcbond_other	1.478
r_angle_other_deg	1.275
r_chiral_restr	0.387
r_bond_refined_d	0.036
r_gen_planes_refined	0.016
r_bond_other_d	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1232
Nucleic Acid Atoms
Solvent Atoms	275
Heterogen Atoms	24

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.