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Structure of variola topoisomerase covalently bound to DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 294 8% PEG 8000, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.523 α = 90 b = 138.232 β = 90 c = 113.079 γ = 90
Symmetry Space Group C 2 2 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 4 2005-04-12 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 4 2005-04-12 M MAD 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 0.97917 ALS 8.2.1 2 SYNCHROTRON ALS BEAMLINE 8.2.1 0.97952, 0.97935, 0.96394 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.7 50 99.5 0.038 29.4 4.3 14945
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 2.7 2.78 99.8 0.199 4.3 1214
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MAD THROUGHOUT 2.7 50 15090 770 99.72 0.193 0.193 0.191 0.2023 0.237 0.2308 RANDOM 68.984
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] -1.3 4.04 -2.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.073 r_dihedral_angle_4_deg 20.93 r_dihedral_angle_3_deg 20.164 r_dihedral_angle_1_deg 5.721 r_scangle_it 1.982 r_angle_refined_deg 1.53 r_scbond_it 1.229 r_mcangle_it 0.915 r_mcbond_it 0.52 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.073 r_dihedral_angle_4_deg 20.93 r_dihedral_angle_3_deg 20.164 r_dihedral_angle_1_deg 5.721 r_scangle_it 1.982 r_angle_refined_deg 1.53 r_scbond_it 1.229 r_mcangle_it 0.915 r_mcbond_it 0.52 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.235 r_nbd_refined 0.225 r_symmetry_hbond_refined 0.154 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.093 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2585 Nucleic Acid Atoms 505 Solvent Atoms 54 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing REFMAC refinement PDB_EXTRACT data extraction