2IXP

Crystal structure of the Pp2A phosphatase activator Ypa1 PTPA1 in complex with model substrate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IXO	PDB ENTRY 2IXO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		1.8MM PEPTIDE, 1M AMMONIUM SULFATE, 3% GLYCEROL, 0.1M ADA PH 6.5

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.886	α = 90
b = 86.886	β = 90
c = 410.626	γ = 120

Symmetry
Space Group	P 65

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	MARRESEARCH			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3		ESRF	ID14-3

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	2.8	20	99.9	0.2	5.7	3.8		42938		2

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 2IXO	2.8	29.12	40651	2158	100	0.233	0.229	0.24	0.302	0.27	RANDOM	2.49

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]
3.01	1.5		3.01		-4.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.375
r_dihedral_angle_3_deg	23.401
r_dihedral_angle_4_deg	23.245
r_dihedral_angle_1_deg	9.045
r_angle_refined_deg	2.466
r_mcbond_it	1.354
r_scangle_it	1.195
r_scbond_it	0.729
r_nbtor_refined	0.343
r_symmetry_vdw_refined	0.292
r_nbd_refined	0.29
r_symmetry_hbond_refined	0.29
r_mcangle_it	0.215
r_xyhbond_nbd_refined	0.196
r_chiral_restr	0.174
r_bond_refined_d	0.026
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10372
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing