5JNV | pdb_00005jnv

Crystal structure of bovine low molecular weight protein tyrosine phosphatase (LMPTP) mutant (W49Y N50E) complexed with HEPES

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PNT

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.944	α = 90
b = 122.939	β = 90
c = 44.888	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	CCD	ADSC QUANTUM 315r		2014-09-14	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	1.52	36.25	96.1	0.08	0.943	9	4.2		24753

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	1.52	1.55	54.1		0.388		2.5

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	1PNT	1.6	36.25	20881	1108	98.43	0.156	0.1536	0.16	0.2004	0.2	RANDOM	21.163

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]
-0.11			0.38		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.311
r_dihedral_angle_4_deg	20.113
r_dihedral_angle_3_deg	14.284
r_dihedral_angle_1_deg	6.941
r_angle_refined_deg	2.951
r_mcangle_it	2.004
r_angle_other_deg	1.338
r_mcbond_it	1.33
r_mcbond_other	1.322
r_chiral_restr	0.194

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.311
r_dihedral_angle_4_deg	20.113
r_dihedral_angle_3_deg	14.284
r_dihedral_angle_1_deg	6.941
r_angle_refined_deg	2.951
r_mcangle_it	2.004
r_angle_other_deg	1.338
r_mcbond_it	1.33
r_mcbond_other	1.322
r_chiral_restr	0.194
r_bond_refined_d	0.035
r_gen_planes_refined	0.017
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1232
Nucleic Acid Atoms
Solvent Atoms	221
Heterogen Atoms	27

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 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.