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Crystal structure of mithramycin analogue MTM SA-5-methyl-Trp in complex with DNA AGAGGCCTCT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JVW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 Reservoir: 10-35% v/v 2-methyl-2,4-pentanediol
Drop: 0.5 mM double-stranded DNA, 1.0 mM MTM analogue, 10 mM sodium cacodylate pH 6.0, 4 mM zinc acetate dihydrate and 2 mM spermine
Crystal Properties Matthews coefficient Solvent content 4.51 72.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.471 α = 90 b = 93.471 β = 90 c = 65.405 γ = 120
Symmetry Space Group P 31 2 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 PIXEL DECTRIS EIGER X 9M 2023-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.979 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.23 50 100 1 39 8.2 16410 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.23 2.27 0.779
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 MOLECULAR REPLACEMENT THROUGHOUT 2.23 40.47 15522 840 99.76 0.22869 0.22752 0.2322 0.24937 0.2562 RANDOM 54.851
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] -13.38 -13.38 26.75
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 3.131 r_long_range_B_other 2.483 r_scangle_other 1.443 r_scbond_it 1.178 r_scbond_other 1.171 r_angle_refined_deg 1.124 r_angle_other_deg 1.098 r_chiral_restr 0.048 r_mcbond_other 0.02 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 3.131 r_long_range_B_other 2.483 r_scangle_other 1.443 r_scbond_it 1.178 r_scbond_other 1.171 r_angle_refined_deg 1.124 r_angle_other_deg 1.098 r_chiral_restr 0.048 r_mcbond_other 0.02 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 1212 Solvent Atoms 90 Heterogen Atoms 562
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing