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Topoisomerase VI-B, ADP AlF4- bound dimer form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MX0 PDB entry 1MX0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 292 Tris-HCl, LiSO4, PEG-4000, glycerol, MgCl2, AlCl2, NaF, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.55 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.077 α = 90 b = 74.077 β = 90 c = 344.381 γ = 120
Symmetry Space Group P 32 1 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 2003-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.116 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 30 98.7 0.06 20.1 4 72958 72958 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 2.07 98.9 0.232 4.2 3.5 7206
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 1MX0 2 30 1 69172 69172 3678 98.7 0.18092 0.18092 0.17948 0.1834 0.20801 0.2079 RANDOM 16.549
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] -0.52 -0.26 -0.52 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.345 r_scangle_it 3.422 r_scbond_it 2.042 r_mcangle_it 1.157 r_angle_refined_deg 1.102 r_mcbond_it 0.62 r_symmetry_hbond_refined 0.254 r_symmetry_vdw_refined 0.215 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.345 r_scangle_it 3.422 r_scbond_it 2.042 r_mcangle_it 1.157 r_angle_refined_deg 1.102 r_mcbond_it 0.62 r_symmetry_hbond_refined 0.254 r_symmetry_vdw_refined 0.215 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.117 r_chiral_restr 0.088 r_metal_ion_refined 0.036 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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_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 7449 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing