2FUF

Crystal structure of the SV40 large T antigen origin-binding domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TBD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.72981.6 M Sodium citrate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3447.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.669α = 90
b = 83.669β = 90
c = 35.88γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315crystal2005-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.9793NSLSX29A

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.455098.70.070.0753.610.9253062479623.3
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)RedundancyNumber Unique Reflections (All)
11.451.596.396.30.4410.4414.59.72416

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 DIFFRACTIONSADTHROUGHOUT1TBD1.45502530624796125298.740.170.170.1690.189RANDOM19.648
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]
-0.2-0.1-0.20.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.999
r_dihedral_angle_3_deg12.112
r_dihedral_angle_4_deg7.742
r_dihedral_angle_1_deg6
r_scangle_it2.671
r_scbond_it1.791
r_mcangle_it1.195
r_angle_refined_deg1.141
r_mcbond_it0.716
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.999
r_dihedral_angle_3_deg12.112
r_dihedral_angle_4_deg7.742
r_dihedral_angle_1_deg6
r_scangle_it2.671
r_scbond_it1.791
r_mcangle_it1.195
r_angle_refined_deg1.141
r_mcbond_it0.716
r_nbtor_refined0.307
r_symmetry_vdw_refined0.212
r_nbd_refined0.199
r_symmetry_hbond_refined0.151
r_xyhbond_nbd_refined0.096
r_chiral_restr0.082
r_bond_refined_d0.008
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1029
Nucleic Acid Atoms
Solvent Atoms170
Heterogen Atoms13

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction