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The Pairing Geometry of the Hydrophobic Thymine Analog 2,4-Difluorotoluene in Duplex DNA as Analyzed by X-ray Crystallography
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D0P PDB ID 3D0P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 291 0.1 M NaOAc 3H2O (pH 4.6) and 8% (w/v) PEG 4000
, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.82 56.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.178 α = 90 b = 66.714 β = 121.04 c = 77.571 γ = 90
Symmetry Space Group C 1 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 CCD MARMOSAIC 225 mm CCD 2008-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F
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 1.61 50 98.1 0.053 39.4 7.5 53844 52821
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.61 1.64 0.56 1.7 4.6 2203
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 using MOLREP THROUGHOUT PDB ID 3D0P 1.61 49.39 50108 2690 100 0.19929 0.19721 0.1951 0.23837 0.2371 RANDOM 16.68
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] -0.58 -0.69 -0.94 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.772 r_dihedral_angle_3_deg 14.637 r_dihedral_angle_4_deg 14.398 r_dihedral_angle_1_deg 6.241 r_scangle_it 4.664 r_scbond_it 3.429 r_angle_refined_deg 2.536 r_mcangle_it 2.359 r_mcbond_it 1.457 r_chiral_restr 0.185
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.772 r_dihedral_angle_3_deg 14.637 r_dihedral_angle_4_deg 14.398 r_dihedral_angle_1_deg 6.241 r_scangle_it 4.664 r_scbond_it 3.429 r_angle_refined_deg 2.536 r_mcangle_it 2.359 r_mcbond_it 1.457 r_chiral_restr 0.185 r_bond_refined_d 0.03 r_gen_planes_refined 0.016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2154 Nucleic Acid Atoms 486 Solvent Atoms 231 Heterogen Atoms 24
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling