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Crystal structure of d(GCGAACGC): two types of bulge-containing duplexes
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 40mM sodium cacodylate, 12mM spermine tetrahydrochloride, 80mM sodium chloride, 10%(v/v) 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.24 43.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.83 α = 90 b = 26.83 β = 90 c = 226.325 γ = 120
Symmetry Space Group P 61 2 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 ADSC QUANTUM 4 2000-11-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B 1.00, 0.91955, 0.92010 Photon Factory BL-18B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.602 25.147 93 0.054 0.054 8.2 15.6 1730
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.6 2.74 64.9 0.266 0.266 2.5 12.7 163
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 THROUGHOUT 2.602 25.147 1726 158 92.9 0.254 0.253 0.257 0.269 0.2697 RANDOM 30.435
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] 1.36 0.68 1.36 -2.04
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.841 r_scbond_it 3.061 r_angle_refined_deg 2.654 r_angle_other_deg 2.045 r_symmetry_vdw_other 0.42 r_nbd_other 0.221 r_xyhbond_nbd_refined 0.185 r_chiral_restr 0.182 r_nbd_refined 0.171 r_symmetry_hbond_refined 0.12
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.841 r_scbond_it 3.061 r_angle_refined_deg 2.654 r_angle_other_deg 2.045 r_symmetry_vdw_other 0.42 r_nbd_other 0.221 r_xyhbond_nbd_refined 0.185 r_chiral_restr 0.182 r_nbd_refined 0.171 r_symmetry_hbond_refined 0.12 r_symmetry_vdw_refined 0.118 r_nbtor_other 0.112 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 378 Solvent Atoms 5 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction DPS data reduction MOSFLM data reduction CCP4 data scaling SOLVE phasing