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Structural and functional analysis of the E. coli NusB-S10 transcription antitermination complex.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TZV PDB ID 1TZV and PDB ID 1J5E (chain J) experimental model PDB 1J5E PDB ID 1TZV and PDB ID 1J5E (chain J)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.8 293 0.1 M CHES, pH 8.8, 18 % PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.74 α = 90 b = 48.99 β = 90 c = 112.77 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 100 CCD MARMOSAIC 225 mm CCD mirrors 2006-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9051 SLS X10SA
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 1.3 30 100 0.074 0.074 17.5 15.3 56411 56411
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 1.3 1.4 100 0.648 0.648 5.3 14.6
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 (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 ID 1TZV and PDB ID 1J5E (chain J) 1.3 20 56394 53574 2820 100 0.17504 0.17348 0.1717 0.20448 0.2026 RANDOM 24.51
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] 0.34 0.19 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.796 r_dihedral_angle_4_deg 17.802 r_dihedral_angle_3_deg 14.893 r_dihedral_angle_1_deg 5.737 r_scangle_it 3.575 r_scbond_it 2.472 r_angle_refined_deg 1.512 r_mcangle_it 1.312 r_mcbond_it 0.854 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.796 r_dihedral_angle_4_deg 17.802 r_dihedral_angle_3_deg 14.893 r_dihedral_angle_1_deg 5.737 r_scangle_it 3.575 r_scbond_it 2.472 r_angle_refined_deg 1.512 r_mcangle_it 1.312 r_mcbond_it 0.854 r_nbtor_refined 0.309 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.168 r_symmetry_vdw_refined 0.166 r_symmetry_hbond_refined 0.161 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 1779 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection XDS data reduction XDS data scaling MOLREP phasing