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Promiscuity and specificity in DNA binding to SSB: Insights from the structure of the Mycobacterium smegmatis SSB-ssDNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X3E PDB ENTRY 1X3E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 100mM Hepes, pH7.5, 30% PEG200, 22% PEG4000, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.07 40.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.33 α = 90 b = 112.33 β = 90 c = 48.49 γ = 90
Symmetry Space Group P 43 21 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 IMAGE PLATE MAR scanner 345 mm plate 2009-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 30 99.6 0.101 15.8 6.6 8062 8048 76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.95 99.1 0.543 2.7 5.4 1135
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1X3E 2.8 30 7654 370 99.52 0.24035 0.23839 0.2333 0.28305 0.2813 RANDOM 65.384
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] -0.29 -0.29 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.597 r_dihedral_angle_4_deg 20.67 r_dihedral_angle_3_deg 16.275 r_dihedral_angle_1_deg 4.528 r_scangle_it 3.999 r_mcangle_it 3.339 r_scbond_it 2.76 r_mcbond_it 2.349 r_angle_refined_deg 1.805 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.597 r_dihedral_angle_4_deg 20.67 r_dihedral_angle_3_deg 16.275 r_dihedral_angle_1_deg 4.528 r_scangle_it 3.999 r_mcangle_it 3.339 r_scbond_it 2.76 r_mcbond_it 2.349 r_angle_refined_deg 1.805 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.305 r_nbd_refined 0.284 r_symmetry_hbond_refined 0.222 r_xyhbond_nbd_refined 0.196 r_chiral_restr 0.107 r_bond_refined_d 0.019 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1656 Nucleic Acid Atoms 507 Solvent Atoms 73 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling