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The origin binding domain of the SV40 large T antigen bound non specifically to a 17 bp palindrome DNA (sites 1 and 3)
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, HANGING DROP 7.5 297 20 mM NaAcetate, 20% PEG 3000 + 4% PEG 600, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.72 54.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.87 α = 90 b = 43.87 β = 90 c = 238.308 γ = 90
Symmetry Space Group P 43 21 2
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 2004-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.25 20 94 0.044 18.1 3.6 11307 11307 -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) 2.25 2.33 93 0.439 2.1
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 1IPR 2.3 19.92 10057 518 94.61 0.23999 0.23682 0.2329 0.29895 0.3031 RANDOM 43.138
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] 0.14 0.14 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.013 r_dihedral_angle_3_deg 19.284 r_dihedral_angle_4_deg 18.005 r_dihedral_angle_1_deg 7.687 r_scangle_it 3.853 r_scbond_it 2.563 r_angle_refined_deg 2.191 r_mcangle_it 1.788 r_mcbond_it 1.015 r_symmetry_vdw_refined 0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.013 r_dihedral_angle_3_deg 19.284 r_dihedral_angle_4_deg 18.005 r_dihedral_angle_1_deg 7.687 r_scangle_it 3.853 r_scbond_it 2.563 r_angle_refined_deg 2.191 r_mcangle_it 1.788 r_mcbond_it 1.015 r_symmetry_vdw_refined 0.325 r_nbtor_refined 0.315 r_nbd_refined 0.252 r_symmetry_hbond_refined 0.22 r_xyhbond_nbd_refined 0.185 r_chiral_restr 0.12 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 961 Nucleic Acid Atoms 363 Solvent Atoms 82 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling