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Human DNA Topoisomerase I (70 Kda) In Complex With The Poison Camptothecin and Covalent Complex With A 22 Base Pair DNA Duplex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K4T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 289 PEG 8000, ammonium sulfate, MES, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.9 57.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.363 α = 90 b = 114.423 β = 93.49 c = 74.118 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 32-ID APS 32-ID
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 3 20 91 0.08 13.7 16492 16492
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) 3 3.16 47 0.427 1.7 1427
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1K4T 3 20 16492 900 90.91 0.24356 0.2409 0.29154 RANDOM 72.185
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] -2.1 3.41 -3.25 5.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 22.299 r_dihedral_angle_1_deg 3.449 r_scangle_it 3.426 r_angle_refined_deg 1.859 r_scbond_it 1.83 r_mcangle_it 1.41 r_mcbond_it 0.744 r_nbd_refined 0.329 r_xyhbond_nbd_refined 0.246 r_symmetry_vdw_refined 0.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 22.299 r_dihedral_angle_1_deg 3.449 r_scangle_it 3.426 r_angle_refined_deg 1.859 r_scbond_it 1.83 r_mcangle_it 1.41 r_mcbond_it 0.744 r_nbd_refined 0.329 r_xyhbond_nbd_refined 0.246 r_symmetry_vdw_refined 0.234 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_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_refined 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 4687 Nucleic Acid Atoms 892 Solvent Atoms Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling AMoRE phasing