2IPR | pdb_00002ipr

Origin binding domain of the SV40 large T antigen (residues 131-259). P21 crystal form

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.1	300	20 mM NaSCN, 10% P4K, 0.1 Tris, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.715	α = 90
b = 56.633	β = 97.13
c = 59.889	γ = 90

Symmetry
Space Group	P 1 21 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	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2003-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	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	1.5	59.76	98.5	0.036	33.9	3.4	39574	39574		-3

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)
	1.5	1.55	94.2		0.165	7.7		3753

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 (All)	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	MIR	THROUGHOUT	NONE	1.5	59.76	37588	1971	98.51	0.17901	0.17901	0.17772	0.1807	0.20427	0.208	RANDOM	16.404

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]
-0.27		0.08	0.08		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.289
r_scangle_it	3.445
r_scbond_it	2.137
r_mcangle_it	1.512
r_angle_refined_deg	1.422
r_mcbond_it	0.857
r_angle_other_deg	0.809
r_symmetry_vdw_other	0.305
r_nbd_other	0.246
r_nbd_refined	0.209
r_symmetry_vdw_refined	0.207
r_symmetry_hbond_refined	0.099
r_chiral_restr	0.094
r_xyhbond_nbd_refined	0.094
r_nbtor_other	0.083
r_bond_refined_d	0.012
r_gen_planes_other	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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	2054
Nucleic Acid Atoms
Solvent Atoms	251
Heterogen Atoms

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASES	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling