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Crystal structure of mithramycin analogue MTM SA-Phe in complex with a 10-mer DNA AGGGATCCCT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294 Incubated against 35% v/v 2-methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 6.42 80.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.38 α = 90 b = 49.38 β = 90 c = 128.295 γ = 90
Symmetry Space Group P 43 21 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 MARMOSAIC 300 mm CCD 2014-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.98 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.1 50 99.6 0.13 25.9 14.6 3055
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 SAD THROUGHOUT 3.1 30 3055 156 99.63 0.27973 0.27932 0.2747 0.28824 0.2878 RANDOM 12.121
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] -2.21 -2.21 4.42
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 2.146 r_long_range_B_other 2.145 r_angle_refined_deg 1.969 r_angle_other_deg 1.394 r_scangle_other 0.901 r_scbond_it 0.53 r_scbond_other 0.529 r_mcbond_other 0.199 r_chiral_restr 0.063 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 2.146 r_long_range_B_other 2.145 r_angle_refined_deg 1.969 r_angle_other_deg 1.394 r_scangle_other 0.901 r_scbond_it 0.53 r_scbond_other 0.529 r_mcbond_other 0.199 r_chiral_restr 0.063 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.004 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcangle_it r_mcangle_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 404 Solvent Atoms 20 Heterogen Atoms 341
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing