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Structure of the second Single Stranded DNA Binding protein (SSBb) from Mycobacterium smegmatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EIV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 298 0.2M calcium chloride dihydrate, 0.1M HEPES pH 7.5, 7.5 % (v/v) PEG 400, 3% (w/v) 1,5-diaminopentane dihydrochloride
Crystal Properties Matthews coefficient Solvent content 2.22 39.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.61 α = 90 b = 73.61 β = 90 c = 216.21 γ = 120
Symmetry Space Group P 65 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 IMAGE PLATE MAR scanner 345 mm plate mirrors 2015-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5419
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) CC (Half) 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 2.5 43.24 99.9 0.093 0.093 0.999 16.4 9.9 12839 2 54.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 100 0.1 0.671 2.3 9.6
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 3EIV 2.5 43.24 12140 624 99.91 0.21334 0.21123 0.2167 0.25627 0.2613 RANDOM 54.635
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] 0.08 0.04 0.08 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.482 r_dihedral_angle_4_deg 22.772 r_dihedral_angle_3_deg 19.685 r_long_range_B_other 11.132 r_long_range_B_refined 11.123 r_scangle_other 8.291 r_mcangle_other 7.764 r_mcangle_it 7.761 r_dihedral_angle_1_deg 7.358 r_scbond_it 5.555
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.482 r_dihedral_angle_4_deg 22.772 r_dihedral_angle_3_deg 19.685 r_long_range_B_other 11.132 r_long_range_B_refined 11.123 r_scangle_other 8.291 r_mcangle_other 7.764 r_mcangle_it 7.761 r_dihedral_angle_1_deg 7.358 r_scbond_it 5.555 r_scbond_other 5.552 r_mcbond_it 5.211 r_mcbond_other 5.183 r_angle_refined_deg 1.775 r_angle_other_deg 1.163 r_chiral_restr 0.105 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1493 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing