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Crystal structure of mithramycin analogue MTM SA-Phe in complex with a 10-mer DNA AGGGTACCCT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294 Incubation against against 35% v/v 2-methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 6.57 81.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.564 α = 90 b = 50.564 β = 90 c = 125.243 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 2014-07-14 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 2.4 50 97.7 0.078 35.9 9.3 6349
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 2.4 40 6349 373 98.25 0.26353 0.2619 0.2662 0.28905 0.2887 RANDOM 42.923
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] 0.96 0.96 -1.93
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.658 r_long_range_B_other 5.654 r_scangle_other 4.291 r_scbond_it 3.529 r_scbond_other 3.349 r_angle_other_deg 2.224 r_angle_refined_deg 1.745 r_mcbond_other 0.244 r_chiral_restr 0.063 r_gen_planes_refined 0.012
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 5.658 r_long_range_B_other 5.654 r_scangle_other 4.291 r_scbond_it 3.529 r_scbond_other 3.349 r_angle_other_deg 2.224 r_angle_refined_deg 1.745 r_mcbond_other 0.244 r_chiral_restr 0.063 r_gen_planes_refined 0.012 r_bond_refined_d 0.009 r_bond_other_d 0.008 r_gen_planes_other 0.002 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 407 Solvent Atoms 10 Heterogen Atoms 342
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing