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Crystal Structure of sv40 large T antigen origin binding domain with DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other t antigen origin binding domain and four base pairs duplex dna
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 273 0.1 M sodium cacodylate pH 6.5, 0.1 M calcium acetate, 30 % v/v peg 8000, 20 % glycerol, VAPOR DIFFUSION, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.42 49.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.489 α = 90 b = 68.341 β = 90 c = 97.262 γ = 90
Symmetry Space Group P 21 21 21
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 2005-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.1 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 2.4 40 90.1 0.1 0.1 2.1 12.2 15755 15314 2.1
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 MOLECULAR REPLACEMENT THROUGHOUT t antigen origin binding domain and four base pairs duplex dna 2.4 38.84 15755 14921 772 90.24 0.2088 0.2088 0.2049 0.2055 0.28692 0.2122 RANDOM 53.054
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] -0.98 -4.37 5.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.099 r_dihedral_angle_4_deg 24.621 r_dihedral_angle_3_deg 19.29 r_dihedral_angle_1_deg 8.012 r_scangle_it 2.866 r_angle_refined_deg 2.013 r_scbond_it 1.868 r_mcangle_it 1.575 r_mcbond_it 0.878 r_symmetry_hbond_refined 0.459
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.099 r_dihedral_angle_4_deg 24.621 r_dihedral_angle_3_deg 19.29 r_dihedral_angle_1_deg 8.012 r_scangle_it 2.866 r_angle_refined_deg 2.013 r_scbond_it 1.868 r_mcangle_it 1.575 r_mcbond_it 0.878 r_symmetry_hbond_refined 0.459 r_nbtor_refined 0.314 r_nbd_refined 0.239 r_xyhbond_nbd_refined 0.208 r_symmetry_vdw_refined 0.192 r_chiral_restr 0.108 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2063 Nucleic Acid Atoms 855 Solvent Atoms 77 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling