2IPR

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.130020 mM NaSCN, 10% P4K, 0.1 Tris, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.0640.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.715α = 90
b = 56.633β = 97.13
c = 59.889γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVmirrors2003-07-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.559.7698.50.03633.93.43957439574-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.51.5594.20.1657.73753

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMIRTHROUGHOUTNONE1.559.7637588197198.510.179010.179010.177720.20427RANDOM16.404
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]
-0.270.080.080.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.289
r_scangle_it3.445
r_scbond_it2.137
r_mcangle_it1.512
r_angle_refined_deg1.422
r_mcbond_it0.857
r_angle_other_deg0.809
r_symmetry_vdw_other0.305
r_nbd_other0.246
r_nbd_refined0.209
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.289
r_scangle_it3.445
r_scbond_it2.137
r_mcangle_it1.512
r_angle_refined_deg1.422
r_mcbond_it0.857
r_angle_other_deg0.809
r_symmetry_vdw_other0.305
r_nbd_other0.246
r_nbd_refined0.209
r_symmetry_vdw_refined0.207
r_symmetry_hbond_refined0.099
r_chiral_restr0.094
r_xyhbond_nbd_refined0.094
r_nbtor_other0.083
r_bond_refined_d0.012
r_gen_planes_other0.011
r_gen_planes_refined0.009
r_bond_other_d0.002
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 AtomsNumber
Protein Atoms2054
Nucleic Acid Atoms
Solvent Atoms251
Heterogen Atoms

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASESphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling