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Topoisomerase VI-B, ADP-bound monomer form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MU5 PDB entry 1MU5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 292 HEPES, NaCl, Mg(HCO2)2, PEG-3350, MgCl2, ADP, pH 7.5, Microbatch, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.78 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.573 α = 90 b = 112.451 β = 90 c = 56.079 γ = 90
Symmetry Space Group P 21 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 CCD ADSC QUANTUM 210 2003-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.100 ALS 8.3.1
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 2.1 30 99.1 0.1 12.1 35386 35386 1 1
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 2.1 2.18 99.9 0.369 3.3 3474
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB entry 1MU5 2.1 29.62 1 32440 32440 2916 99.18 0.19244 0.19244 0.18925 0.1925 0.22763 0.2269 RANDOM 20.83
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] -1.88 0.01 1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.355 r_scangle_it 4.338 r_scbond_it 2.657 r_mcangle_it 1.339 r_angle_refined_deg 1.171 r_mcbond_it 0.704 r_symmetry_vdw_refined 0.239 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.355 r_scangle_it 4.338 r_scbond_it 2.657 r_mcangle_it 1.339 r_angle_refined_deg 1.171 r_mcbond_it 0.704 r_symmetry_vdw_refined 0.239 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.098 r_symmetry_hbond_refined 0.059 r_bond_refined_d 0.02 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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 3696 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing