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Topoisomerase VI-B, ADP Pi 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 K2HPO4, PEG-3350, MPD, MgCl2, 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 = 74.503 α = 90 b = 74.503 β = 90 c = 346.458 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 2002-06-16 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 2.2 30 94.6 0.059 23.4 4.6 53646 53646 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 2.28 97.3 0.248 5.9 4.6 5432
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 2.2 20 1 50547 50547 2690 94.16 0.19632 0.19632 0.19443 0.1945 0.23222 0.229 RANDOM 30.841
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] 0.22 0.11 0.22 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.696 r_scangle_it 4.351 r_scbond_it 2.768 r_mcangle_it 1.538 r_angle_refined_deg 1.364 r_mcbond_it 0.841 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.221 r_xyhbond_nbd_refined 0.153 r_symmetry_hbond_refined 0.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.696 r_scangle_it 4.351 r_scbond_it 2.768 r_mcangle_it 1.538 r_angle_refined_deg 1.364 r_mcbond_it 0.841 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.221 r_xyhbond_nbd_refined 0.153 r_symmetry_hbond_refined 0.143 r_chiral_restr 0.129 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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 7421 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing