3JS5 | pdb_00003js5

Crystal structure of protein tyrosine phosphatase from Entamoeba histolytica with Hepes in the active site. High resolution, alternative crystal form with 1 molecule in asymmetric unit

X-RAY DIFFRACTION

---

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	PACT screen condition E6, 20% PEG 3350, 0.2 M sodium formate. 0.4:0.4 microliter drops. 31.7 mg/mL protein in 25 mM Hepes pH 7.0, 0.3 M NaCl, 10% Glycerol, 2 mM DTT. Crystal tracking ID 204749e6, expression tag not removed prior to crystallization, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.433	α = 90
b = 60.195	β = 90
c = 72.229	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	RIGAKU SATURN 944		2009-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	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	1.94	50	97.9	0.066	19.6	4.4		12697

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	1.94	2.02	84.9		0.198	4.7	2.2	1069

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	1.94	46.24	12657	643	97.82	0.169	0.167	0.178	0.212	0.1782	RANDOM	17.165

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			-0.62		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.049
r_dihedral_angle_3_deg	12.801
r_dihedral_angle_4_deg	12.48
r_dihedral_angle_1_deg	5.335
r_scangle_it	2.663
r_scbond_it	1.636
r_angle_refined_deg	1.087
r_mcangle_it	0.965
r_mcbond_it	0.5
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1245
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms	16

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