3JVI | pdb_00003jvi

Product state mimic crystal structure of protein tyrosine phosphatase from Entamoeba histolytica

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IDO	PDB entry 3IDO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	Emerald Biosystems Wizard II screen condition 41, 2.0 M Ammonium sulfate, 0.1 M Tris-HCl pH 7.0, 0.2 M Lithium sulfate, 26.1 mg/mL protein. Crystal tracking ID 203693h5, expression tag removed with 3C protease, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
1.83	32.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.995	α = 90
b = 44.995	β = 90
c = 133.316	γ = 90

Symmetry
Space Group	P 43 21 2

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	RIGAKU SATURN 944+		2009-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	1.8	50	96.2	0.062	22.84	7.6	13504	12964

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	1.8	1.86	100		0.254	5.71	4.6	1287

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	PDB entry 3IDO	1.8	42.64	12911	644	96.12	0.206	0.204	0.2052	0.249	0.2488	RANDOM	13.914

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]
3.03			3.03		-6.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.639
r_dihedral_angle_3_deg	15.1
r_dihedral_angle_4_deg	14.868
r_dihedral_angle_1_deg	5.272
r_scangle_it	3.249
r_scbond_it	2.115
r_mcangle_it	1.422
r_angle_refined_deg	1.273
r_mcbond_it	0.761
r_chiral_restr	0.098
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1235
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	5

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling