☰ Navigation Tabs
Crystal structure of the C-terminal domain of DNA topoisomerase IV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 magnesium acetate, sodium cacodylate, MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.211 α = 90 b = 83.211 β = 90 c = 44.999 γ = 120
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 2003-12-07 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL12B2 0.95370, 0.97994, 0.97966 SPring-8 BL12B2
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 1.79 23.3 92.9 0.096 5.3 32512 30204 2 2 22.1
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) 1.8 1.85 70.3 0.224 4.2 1906
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.79 23 2 32512 29086 1548 93.73 0.16262 0.16262 0.1599 0.1716 0.21381 0.219 RANDOM 20.942
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] -0.05 -0.02 -0.05 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.843 r_scangle_it 5.43 r_scbond_it 3.397 r_mcangle_it 2.284 r_angle_refined_deg 1.773 r_mcbond_it 1.278 r_angle_other_deg 0.91 r_symmetry_vdw_other 0.378 r_symmetry_vdw_refined 0.335 r_nbd_other 0.258
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.843 r_scangle_it 5.43 r_scbond_it 3.397 r_mcangle_it 2.284 r_angle_refined_deg 1.773 r_mcbond_it 1.278 r_angle_other_deg 0.91 r_symmetry_vdw_other 0.378 r_symmetry_vdw_refined 0.335 r_nbd_other 0.258 r_symmetry_hbond_refined 0.244 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.216 r_chiral_restr 0.119 r_nbtor_other 0.086 r_bond_refined_d 0.024 r_gen_planes_refined 0.009 r_gen_planes_other 0.007 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_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 2575 Nucleic Acid Atoms Solvent Atoms 377 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SHARP phasing