2ITL

The origin binding domain of the SV40 large T antigen bound to the functional pen palindrome DNA (23 bp)

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	297	20 mM di-ammonium hydrogen citrate, 20% PEG 3000, and 10 mM MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.196	α = 90
b = 64.096	β = 120.69
c = 79.177	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 4		2005-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.9176	CHESS	F1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.65	40	99.6	0.062	23.8	3.6	42961	42961		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.65	1.71	97.7		0.213			4204

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	2IPR	1.65	40	40799	2161	99.57	0.20378	0.2013	0.19	0.25061	0.24	RANDOM	35.282

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]
0.04			-0.28		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.176
r_dihedral_angle_4_deg	21.023
r_dihedral_angle_3_deg	15.159
r_dihedral_angle_1_deg	5.668
r_sphericity_free	5.112
r_sphericity_bonded	4.055
r_scangle_it	3.3
r_rigid_bond_restr	3.012
r_scbond_it	2.774
r_mcangle_it	2.045
r_angle_refined_deg	1.46
r_mcbond_it	1.263
r_symmetry_vdw_refined	0.36
r_nbtor_refined	0.308
r_nbd_refined	0.196
r_symmetry_hbond_refined	0.168
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.095
r_bond_refined_d	0.011
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1921
Nucleic Acid Atoms	979
Solvent Atoms	307
Heterogen Atoms

Software

Software
Software Name	Purpose
CHESS	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling