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Crystal structure of Dickerson Drew Dodecamer with 5-carboxycytosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 436D PDB ID 436D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 40 mM Na Cacodylate, 12 mM Spermine Tetrahydrochloride, 80 mM SrCl2, 10% MPD , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.24 45.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.25 α = 90 b = 41.34 β = 90 c = 66.41 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 100 CCD ADSC QUANTUM 315 2013-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97920 APS 24-ID-C
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 1.95 26 97.5 0.045 16.26 5242 5113 3
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 1.95 2 99.5 0.62 2.8 385
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ID 436D 1.95 25.89 4704 409 97.54 0.22492 0.22129 0.26721 0.3037 RANDOM 45.709
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]
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 8.229 r_long_range_B_other 8.218 r_scangle_other 7.305 r_scbond_it 5.348 r_scbond_other 5.346 r_angle_other_deg 3.717 r_angle_refined_deg 2.209 r_chiral_restr 0.164 r_gen_planes_refined 0.022 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 8.229 r_long_range_B_other 8.218 r_scangle_other 7.305 r_scbond_it 5.348 r_scbond_other 5.346 r_angle_other_deg 3.717 r_angle_refined_deg 2.209 r_chiral_restr 0.164 r_gen_planes_refined 0.022 r_bond_refined_d 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 492 Solvent Atoms 12 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling