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The origin binding domain of the SV40 large T antigen bound to the functional pen palindrome DNA (23 bp)
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 0.1937 0.25061 0.243 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
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