2PF4 | pdb_00002pf4

Crystal structure of the full-length simian virus 40 small t antigen complexed with the protein phosphatase 2A Aalpha subunit

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8	298	16% PEG 3350, 0.2 M Ammonium formate, 30 mM spermine, 6% 6-aminocaproic acid, 10 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.00

Crystal Properties
Matthews coefficient	Solvent content
2.67	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.711	α = 115.64
b = 105.501	β = 109.55
c = 111.937	γ = 94.11

Symmetry
Space Group	P 1

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 210		2007-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1		ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	3.1	50	98	0.076	0.076	12.1	7.1		62693		1.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.1	3.21	88.7		0.758	0.758	1.8	4.8

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2IAE-A	3.1	20	59306	3159	97.4	0.247	0.244	0.24	0.304	RANDOM	114.44

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]
3.04	-0.5	1.94	-2.8	-1.19	-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.301
r_dihedral_angle_3_deg	20.662
r_dihedral_angle_4_deg	19.111
r_dihedral_angle_1_deg	5.855
r_scangle_it	1.563
r_angle_refined_deg	1.387
r_scbond_it	0.933
r_mcangle_it	0.704
r_mcbond_it	0.391
r_nbtor_refined	0.303
r_nbd_refined	0.243
r_symmetry_vdw_refined	0.238
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.091
r_symmetry_hbond_refined	0.08
r_metal_ion_refined	0.018
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	22794
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	8

Software

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