5JNW | pdb_00005jnw

Crystal structure of bovine low molecular weight protein tyrosine phosphatase (LMPTP) mutant (W49Y N50E) complexed with vanadate and uncompetitive inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5JNV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	6.5	293	20% PEG 3350, 0.2 M NaCl, Bis Tris

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.347	α = 90
b = 125.493	β = 90
c = 45.251	γ = 90

Symmetry
Space Group	C 2 2 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	PIXEL	DECTRIS PILATUS 6M		2016-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.0	SSRL	BL9-2

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	1.86	36.7	96.6	0.057	0.996	12.7	4.2		14411

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	1.86	1.9	60.3		0.449		3.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5JNV	1.86	36.7	13691	710	96.53	0.1683	0.1663	0.18	0.2095	0.21	RANDOM	31.982

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]
-1.92			1.5		0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.258
r_dihedral_angle_4_deg	18.572
r_dihedral_angle_3_deg	15.067
r_dihedral_angle_1_deg	7.104
r_angle_refined_deg	2.829
r_mcangle_it	2.673
r_mcbond_it	1.969
r_mcbond_other	1.966
r_angle_other_deg	1.408
r_chiral_restr	0.201

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.258
r_dihedral_angle_4_deg	18.572
r_dihedral_angle_3_deg	15.067
r_dihedral_angle_1_deg	7.104
r_angle_refined_deg	2.829
r_mcangle_it	2.673
r_mcbond_it	1.969
r_mcbond_other	1.966
r_angle_other_deg	1.408
r_chiral_restr	0.201
r_bond_refined_d	0.034
r_gen_planes_refined	0.015
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1232
Nucleic Acid Atoms
Solvent Atoms	153
Heterogen Atoms	60

Software

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

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.