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Crystal structure of the DB921-D(CGCGAATTCGCG)2 complex.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DBE DNA PART OF NDB ENTRY GDL009 OR PDB ENTRY 2DBE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 293 MAGNESIUM CHLORIDE, DNA, COMPOUND DB921, MPD, SODIUM CACODYLATE BUFFER, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K, pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.69 54.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.288 α = 90 b = 40.068 β = 90 c = 65.989 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 105 IMAGE PLATE RIGAKU RAXIS IV OSMIC FOCUSING MIRROR SYSTEM 2005-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.64 25 96.6 0.056 36.19 3.16 8055 -2
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) 1.64 1.7 96.4 0.197 6.43
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 DNA PART OF NDB ENTRY GDL009 OR PDB ENTRY 2DBE 1.64 8 2 7968 784 87.2 0.2307 0.2286 0.2287 0.3002 0.2839 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 596
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.067 s_non_zero_chiral_vol 0.037 s_anti_bump_dis_restr 0.026 s_angle_d 0.019 s_from_restr_planes 0.009 s_bond_d 0.004 s_similar_dist s_zero_chiral_vol s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 486 Solvent Atoms 76 Heterogen Atoms 34
Software Software Software Name Purpose SHELXL-97 refinement SCALEPACK data scaling CNS refinement DENZO data reduction CNS phasing