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Crystal structure of the SV40 large T antigen origin-binding domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TBD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 298 1.6 M Sodium citrate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.34 47.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.669 α = 90 b = 83.669 β = 90 c = 35.88 γ = 120
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 crystal 2005-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9793 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 1.45 50 98.7 0.07 0.07 53.6 10.9 25306 24796 23.3
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) Redundancy Number Unique Reflections (All) 1 1.45 1.5 96.3 96.3 0.441 0.441 4.5 9.7 2416
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-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1TBD 1.45 50 25306 24796 1252 98.74 0.17 0.17 0.169 0.1685 0.189 0.1859 RANDOM 19.648
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 -0.2 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.999 r_dihedral_angle_3_deg 12.112 r_dihedral_angle_4_deg 7.742 r_dihedral_angle_1_deg 6 r_scangle_it 2.671 r_scbond_it 1.791 r_mcangle_it 1.195 r_angle_refined_deg 1.141 r_mcbond_it 0.716 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.999 r_dihedral_angle_3_deg 12.112 r_dihedral_angle_4_deg 7.742 r_dihedral_angle_1_deg 6 r_scangle_it 2.671 r_scbond_it 1.791 r_mcangle_it 1.195 r_angle_refined_deg 1.141 r_mcbond_it 0.716 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.212 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.096 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1029 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 13
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction