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SV40 Large T antigen origin binding domain bound to artificial DNA fork
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FUF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 100 mM Tris, 300 mM NH4Cl, 28% polyethylene glycol [PEG] 4000, 20 mM CaCl2
Crystal Properties Matthews coefficient Solvent content 2.18 43.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.192 α = 90 b = 63.393 β = 92.42 c = 64.891 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 315r 2009-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0809 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 50 88.8 15.9 7.3 37425
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 54.7 4.6
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 2FUF 1.7 50 35570 1895 88.7 0.18174 0.17965 0.191 0.22257 0.2353 RANDOM 35.147
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] 1.89 -1.15 -0.66 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.799 r_dihedral_angle_4_deg 12.281 r_dihedral_angle_3_deg 12.164 r_long_range_B_refined 6.652 r_dihedral_angle_1_deg 6.625 r_long_range_B_other 6.606 r_scangle_other 4.097 r_scbond_it 2.744 r_scbond_other 2.743 r_mcangle_other 2.485
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.799 r_dihedral_angle_4_deg 12.281 r_dihedral_angle_3_deg 12.164 r_long_range_B_refined 6.652 r_dihedral_angle_1_deg 6.625 r_long_range_B_other 6.606 r_scangle_other 4.097 r_scbond_it 2.744 r_scbond_other 2.743 r_mcangle_other 2.485 r_mcangle_it 2.483 r_mcbond_it 1.859 r_mcbond_other 1.855 r_angle_refined_deg 1.709 r_angle_other_deg 1.479 r_chiral_restr 0.11 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.006 r_gen_planes_other 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2162 Nucleic Acid Atoms 896 Solvent Atoms 230 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing