2IF9 | pdb_00002if9

Crystal Structure of SV40 T-antigen origin binding domain disulfide-linked dimer

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	30 % peg 4000, 0.1M sodium citrate (pH 5.6), 0.2 M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.463	α = 90
b = 63.982	β = 94.45
c = 63.228	γ = 90

Symmetry
Space Group	C 1 2 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 315	2005-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9791	NSLS	X29A

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	2.586	50	85.1	0.126	0.126	7.7	3	7348	7009

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)
	2.586	2.69	53.3		0.215	0.215	2.4	2.4	458

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2FUF	2.586	38.63	7345	7009	336	85.22	0.213	0.208	0.2064	0.296	0.2798	RANDOM	28.493

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]
0.17		-0.02	-0.08		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.413
r_dihedral_angle_4_deg	19.714
r_dihedral_angle_3_deg	17.722
r_dihedral_angle_1_deg	7.905
r_scangle_it	2.377
r_scbond_it	1.506
r_angle_refined_deg	1.463
r_mcangle_it	1.105
r_mcbond_it	0.616
r_nbtor_refined	0.315
r_nbd_refined	0.231
r_symmetry_vdw_refined	0.203
r_xyhbond_nbd_refined	0.193
r_symmetry_hbond_refined	0.136
r_chiral_restr	0.098
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2144
Nucleic Acid Atoms
Solvent Atoms	51
Heterogen Atoms

Software

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