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The effect of Berenil and Cacodylateon the crystal structure of d(CGTGAATTCACG)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D29
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 290 60mM Sodium cacodylate, 17mM MgCl2, 2m M Spermine, 50% MPD, 1.5mM Berenil
Crystal Properties Matthews coefficient Solvent content 2.3 46.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 25.044 α = 90 b = 41.534 β = 90 c = 64.868 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD AGILENT ATLAS CCD 2017-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION NOVA 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 34.98 100 4 8.6 3731
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1D29 2.3 34.98 3114 150 99.39 0.24765 0.24462 0.2468 0.31207 0.3176 RANDOM 31.768
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] -0.02 0.05 -0.03
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 6.741 r_long_range_B_other 6.723 r_scangle_other 4.115 r_scbond_it 3.208 r_scbond_other 3.207 r_angle_other_deg 1.832 r_angle_refined_deg 1.733 r_chiral_restr 0.091 r_gen_planes_refined 0.015 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 6.741 r_long_range_B_other 6.723 r_scangle_other 4.115 r_scbond_it 3.208 r_scbond_other 3.207 r_angle_other_deg 1.832 r_angle_refined_deg 1.733 r_chiral_restr 0.091 r_gen_planes_refined 0.015 r_bond_refined_d 0.008 r_bond_other_d 0.003 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_mcbond_other 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 486 Solvent Atoms 15 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction SCALA data scaling PHASER phasing