3IDO

Crystal structure of protein tyrosine phosphatase from Entamoeba histolytica with a phosphotyrosine crude mimic HEPES molecule in the active site

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	ProPlex condition F1, 0.1 M Hepes pH 7.0, 20% PEG 8000, 25% glycerol as cryo-protectant, 26.1 mg/mL protein, 0.1 mg/mL chymotrypsin, crystal tracking ID 203694f1, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.579	α = 90
b = 70.409	β = 90
c = 79.189	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		2009-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.9765	ALS	5.0.3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.2	45.93	98.6	0.14	7.7	8.1		17494

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	2.2	2.28	89.5		0.492	2.43	5.7	1539

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	PDB entry 1xww	2.2	45.93	17445	887	98.45	0.206	0.204	0.254	RANDOM	36.713

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]
-2.71			-0.15		2.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.578
r_dihedral_angle_3_deg	14.642
r_dihedral_angle_4_deg	13.839
r_dihedral_angle_1_deg	5.64
r_scangle_it	2.542
r_scbond_it	1.541
r_angle_refined_deg	1.211
r_mcangle_it	1.095
r_mcbond_it	0.576
r_chiral_restr	0.084

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.578
r_dihedral_angle_3_deg	14.642
r_dihedral_angle_4_deg	13.839
r_dihedral_angle_1_deg	5.64
r_scangle_it	2.542
r_scbond_it	1.541
r_angle_refined_deg	1.211
r_mcangle_it	1.095
r_mcbond_it	0.576
r_chiral_restr	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2524
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	30

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

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.