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Crystal structure of Streptococcus pneumoniae FabT in complex with DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 289 0.1 M sodium citrate pH 5.5, 0.2 M Sodium acetate trihydrate, 5% PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.2 61.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.022 α = 90 b = 60.868 β = 105.4 c = 74.086 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2018-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97918 SSRF BL17U
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 2.2 50 98.5 0.085 0.085 0.857 6.2 6.2 31594 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 100 0.54 0.54 0.857 6
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 SAD THROUGHOUT 2.2 35.96 30078 1503 98.59 0.18922 0.18763 0.1939 0.2207 0.2271 RANDOM 43.169
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] -0.17 0.87 -0.25 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.324 r_dihedral_angle_3_deg 16.645 r_dihedral_angle_4_deg 10.664 r_long_range_B_refined 8.507 r_long_range_B_other 8.475 r_scangle_other 7.476 r_scbond_it 5.244 r_scbond_other 5.243 r_dihedral_angle_1_deg 5.173 r_mcangle_it 4.416
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.324 r_dihedral_angle_3_deg 16.645 r_dihedral_angle_4_deg 10.664 r_long_range_B_refined 8.507 r_long_range_B_other 8.475 r_scangle_other 7.476 r_scbond_it 5.244 r_scbond_other 5.243 r_dihedral_angle_1_deg 5.173 r_mcangle_it 4.416 r_mcangle_other 4.416 r_mcbond_it 3.407 r_mcbond_other 3.405 r_angle_refined_deg 1.445 r_angle_other_deg 0.842 r_chiral_restr 0.066 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2358 Nucleic Acid Atoms 935 Solvent Atoms 209 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX model building