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Crystal structure analysis of trioxacarcin A covalently bound to d(AACCGGTT)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 7 313 tri-ammoniumcitrate, DMSO, pH 7.0, hanging drop, temperature 313K
Crystal Properties Matthews coefficient Solvent content 2.5 50.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.6 α = 90 b = 37.6 β = 90 c = 91.62 γ = 90
Symmetry Space Group P 41 2 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 MAR CCD 165 mm 2007-08-08 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.92039, 0.92032, 0.92047 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.67 37.6 99 0.039 0.021 27.81 12.5 8306 8225 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.76 94.7 0.64 0.35 2.92 8.98
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1.78 25.53 6802 314 99.82 0.222 0.22 0.2361 0.265 0.2683 RANDOM 53.16
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] -1.01 -1.01 2.02
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.03 r_angle_refined_deg 2.49 r_scbond_it 2.039 r_angle_other_deg 1.566 r_symmetry_vdw_other 0.304 r_nbtor_refined 0.257 r_nbd_other 0.246 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.163 r_nbtor_other 0.121
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.03 r_angle_refined_deg 2.49 r_scbond_it 2.039 r_angle_other_deg 1.566 r_symmetry_vdw_other 0.304 r_nbtor_refined 0.257 r_nbd_other 0.246 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.163 r_nbtor_other 0.121 r_symmetry_vdw_refined 0.096 r_chiral_restr 0.092 r_symmetry_hbond_refined 0.091 r_gen_planes_refined 0.025 r_bond_refined_d 0.016 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 322 Solvent Atoms 21 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection HKL-2000 data reduction SADABS data scaling SHELXDE phasing