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The Structure of the Dickerson Sequence with an Incorporated CeNA Residue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 355D PDB ENTRY 355D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 289 20mM potassium cacodylate buffer (pH=5.5), 10mM cobalt hexamine, 44mM potassium chloride, 6mM sodium chloride, 5%(v/v) 2-methyl-2,4-pentanediol (MPD), and 0.75mM ssDNA against a 35%(v/v) MPD stock solution, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.12 41.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.915 α = 90 b = 38.78 β = 90 c = 66.923 γ = 90
Symmetry Space Group P 2 2 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 IMAGE PLATE MAR scanner 345 mm plate 2004-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8414 EMBL/DESY, HAMBURG BW7B
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 1.9 20 99.4 0.05 0.05 15.3 4.5 5476 5476 38
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) 1.9 2 100 0.457 0.457 3 4.6 777
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) 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 PDB ENTRY 355D 1.9 17.76 5209 5209 245 99.27 0.23313 0.23313 0.22954 0.2367 0.30752 0.2972 RANDOM 44.161
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] 0.04 -0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.149 r_scbond_it 2.019 r_angle_refined_deg 1.803 r_nbtor_refined 0.324 r_xyhbond_nbd_refined 0.2 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.171 r_symmetry_hbond_refined 0.156 r_chiral_restr 0.087 r_bond_refined_d 0.011
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.149 r_scbond_it 2.019 r_angle_refined_deg 1.803 r_nbtor_refined 0.324 r_xyhbond_nbd_refined 0.2 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.171 r_symmetry_hbond_refined 0.156 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_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 469 Solvent Atoms 74 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection MOSFLM data reduction SCALA data scaling PHASER phasing